Rationale: This script performs differential gene expression (dge) and calculates the upregulated and downregulated genes in different parts of lichen thallus using Sleuth

1. Prepare data

library(sleuth)
library(tidyverse)
samples<-read.delim("../data/metadata/found_samples_in_sequences_db_thallus.csv",sep=",")

kal_dirs2 <- data.frame("sample"=samples$run_id, "part"= samples$sample_focus,
                       substrate=samples$growth_site, thallus = samples$thallus_id,
                       "path"=paste0("../analysis_and_temp_files/06_meta_mapping/kallisto_meta_mapping/",samples$run_id,"_kallisto"))  %>% filter(sample!="MP_I" & sample!="MP_II")
full<-read.delim("../analysis_and_temp_files/08_dge_culture_lichen/counts_table.tsv",row.names=1)
d<-full %>% select(any_of(kal_dirs2$sample)) #include only lichen samples
colnames(d)
##  [1] "XBC2"   "XBA1"   "XSA2_2" "XSC1"   "XSE2"   "XBE1"   "XTA2"   "XSC2"  
##  [9] "XSA2"   "XBA2"   "XBC1"   "XTA1"   "XSA1"   "XTC2"   "XTE2"   "XBE2"  
## [17] "XMC2"
d$max<-apply(d,1,max)
min(d$max)
## [1] 0
d1<-d[which(d$max>=5),] #to remove lowly expressed genes, keep rows in which max read count across whole panel is atleast 5

# drop the max column, as its not needed anymore
raw_counts<-d1 %>% select(-max)
length(rownames(d1)) # total number of genes
## [1] 11083
length(rownames(raw_counts)) 
## [1] 11083
#make the list of selected genes
target_id<-rownames(d1)

2. Edge / Center comparison

ec_dirs<-kal_dirs2 %>% filter(part %in% c("thallus_centre", "thallus_edge") )
ec_dirs$part <- as.factor(ec_dirs$part)

ec_so <- sleuth_prep(ec_dirs,extra_bootstrap_summary = TRUE,filter_target_id = target_id,transformation_function = function(x) log2(x + 0.1))
## Warning in check_num_cores(num_cores): It appears that you are running Sleuth from within Rstudio.
## Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
## If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
## reading in kallisto results
## dropping unused factor levels
## ..........
## normalizing est_counts
## A list of target IDs for filtering was found. Using this for filtering
## 11083 targets passed the filter
## normalizing tpm
## merging in metadata
## summarizing bootstraps
## ..........
#model that includes only confounding variables
ec_so <- sleuth_fit(ec_so, ~thallus, 'reduced') 
## fitting measurement error models
## shrinkage estimation
## 7 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000967-T1, XANPAGTX0501_000969-T1, XANPAGTX0501_000980-T1, XANPAGTX0501_002903-T1, XANPAGTX0501_004641-T1, XANPAGTX0501_005100-T1, XANPAGTX0501_006796-T1
## computing variance of betas
#model that includes only both the confounding variable and the variable of interest
ec_so  <- sleuth_fit(ec_so, ~thallus + part, 'full')
## fitting measurement error models
## shrinkage estimation
## 7 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000967-T1, XANPAGTX0501_000969-T1, XANPAGTX0501_000980-T1, XANPAGTX0501_002903-T1, XANPAGTX0501_004641-T1, XANPAGTX0501_005100-T1, XANPAGTX0501_006796-T1
## computing variance of betas
#compare the models
ec_so <- sleuth_lrt(ec_so, 'reduced', 'full')
ec_so <- sleuth_wt(ec_so, 'partthallus_edge')

plot_pca(ec_so, color_by = 'part', text_labels = TRUE,use_filtered=T)

ec_table <- sleuth_results(ec_so, 'partthallus_edge')
ec_sig <- ec_table %>% tibble::as_tibble() %>% 
  filter( qval <= 0.05, grepl("GTX0501",target_id) ) %>% 
  arrange(desc(b)) %>% mutate(change = if_else(b > 1, "edge", ifelse(b< -1, "centre", "low_logFC")))

table(ec_sig$change)
## 
##    centre low_logFC 
##         9       170
ec_dge<-ec_sig$target_id[ec_sig$change!="low_logFC"]
plot_bootstrap(ec_so, 
               target_id = ec_dge[7], 
               units = "est_counts", 
               color_by = "part")
plot_bootstrap(ec_so, 
               target_id = ec_dge[6], 
               units = "est_counts", 
               color_by = "part")

library(kableExtra)
funannot2<-read.delim2("../../02_long_read_assemblies/analysis_and_temp_files/09_ortho/lichen_enriched_ortho_in_xanpa.tsv",sep="\t")

center_ec_genes<-ec_sig %>% filter(change=="centre") %>%
  left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
  select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
center_ec_genes %>% 
  kable(format = "html", col.names = colnames(center_ec_genes)) %>%
  kable_styling() %>%
  kableExtra::scroll_box(width = "100%", height = "600px")
target_id b InterPro_new CAZyme_new Protease_new KO secreted_consensus lichen_ortho
XANPAGTX0501_005615-T1 -1.009109 NA NA NA FALSE FALSE
XANPAGTX0501_005614-T1 -1.075863 NA NA NA FALSE FALSE
XANPAGTX0501_008007-T1 -1.155943 NA NA NA FALSE FALSE
XANPAGTX0501_002184-T1 -1.173653 NA NA NA FALSE FALSE
XANPAGTX0501_001949-T1 -1.187615 NA NA NA FALSE FALSE
XANPAGTX0501_002506-T1 -1.194636 NA NA NA FALSE FALSE
XANPAGTX0501_008856-T1 -1.278297 IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily NA NA FALSE TRUE
XANPAGTX0501_009886-T1 -1.292990 NA NA NA TRUE FALSE
XANPAGTX0501_009927-T1 -1.619707 NA NA NA FALSE TRUE
plot_bootstrap(ec_so, 
               target_id = ec_sig$target_id[ec_sig$b>0.9], 
               units = "est_counts", 
               color_by = "part")

edge_ec_genes<-ec_sig %>% filter(b>0.9) %>%
  left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
  select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
edge_ec_genes %>% 
  kable(format = "html", col.names = colnames(edge_ec_genes)) %>%
  kable_styling() %>%
  kableExtra::scroll_box(width = "100%", height = "600px")
target_id b InterPro_new CAZyme_new Protease_new KO secreted_consensus lichen_ortho
XANPAGTX0501_001015-T1 0.9022441 IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily NA NA TRUE FALSE

2.2. Power analysis: simple

  • Do we have enough samples for this comparison?
  • Looked at the distribution of (non-corrected) p-values. The graph looks good: close to uniform, with an increase close to 0. If our test was underpowered, we would see an increase of p-vlaues along 0->1, but this is not the case
ggplot(ec_table)+geom_histogram(aes(x=pval))
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 690798 rows containing non-finite values (`stat_bin()`).

  • QQ-plot also looks good
library(MKpower)
qqunif(ec_table$pval, color.line = "orange")

  • However, when looking at corrected p-values (a.k.a. q-values), the graph looks bad
ggplot(ec_table)+geom_histogram(aes(x=qval))
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 690798 rows containing non-finite values (`stat_bin()`).

* Perhaps, this particular comparison is underpowered

library(MKpower)
qqunif(ec_table$qval, color.line = "orange")

3. Center / apothetia comparison

ca_dirs<-kal_dirs2 %>% filter(part %in% c("thallus_centre", "apothecia") )
ca_dirs$part <- as.factor(ca_dirs$part)
ca_dirs$thallus<- as.factor(ca_dirs$thallus)

rhdf5::h5closeAll()
ca_so <- sleuth_prep(ca_dirs,extra_bootstrap_summary = TRUE,filter_target_id = target_id,transformation_function = function(x) log2(x + 0.1))
## Warning in check_num_cores(num_cores): It appears that you are running Sleuth from within Rstudio.
## Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
## If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
## reading in kallisto results
## dropping unused factor levels
## .............
## normalizing est_counts
## A list of target IDs for filtering was found. Using this for filtering
## 11083 targets passed the filter
## normalizing tpm
## merging in metadata
## summarizing bootstraps
## .............
#model that includes only confounding variables
ca_so <- sleuth_fit(ca_so, ~thallus, 'reduced') 
## fitting measurement error models
## shrinkage estimation
## 2 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_004237-T1, XANPAGTX0501_010518-T1
## computing variance of betas
#model that includes only both the confounding variable and the variable of interest
ca_so  <- sleuth_fit(ca_so, ~thallus + part, 'full')
## fitting measurement error models
## shrinkage estimation
## 3 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_004237-T1, XANPAGTX0501_010518-T1, XANPAGTX0501_010086-T1
## computing variance of betas
#compare the models
ca_so <- sleuth_lrt(ca_so, 'reduced', 'full')
ca_so <- sleuth_wt(ca_so, 'partthallus_centre')

plot_pca(ca_so, color_by = 'part', text_labels = TRUE,use_filtered=T)

ca_table <- sleuth_results(ca_so, 'partthallus_centre')
ca_sig <- ca_table %>% tibble::as_tibble() %>% 
  filter( qval <= 0.05, grepl("GTX0501",target_id) ) %>% 
  arrange(desc(b)) %>% mutate(change = if_else(b > 1, "centre", ifelse(b< -1, "apothecium", "low_logFC")))

table(ca_sig$change)
## 
## apothecium     centre  low_logFC 
##        118          1       1928

Upregulated in apothecia

  • Bootstrap of the two genes most overexpressed in the apothecium. Why are the boxes so wide?
plot_bootstrap(ca_so, 
               target_id = ca_sig$target_id[which.min(ca_sig$b)], 
               units = "est_counts", 
               color_by = "part")
plot_bootstrap(ca_so, 
               target_id = ca_sig$target_id[which.min(ca_sig$b[-which.min(ca_sig$b)])], 
               units = "est_counts", 
               color_by = "part")

  • Both MAT genes seem upregulated, although XANPAGTX0501_002103-T1 is just below the threshold -0.99
plot_bootstrap(ca_so, 
               target_id = "XANPAGTX0501_002103-T1", 
               units = "est_counts", 
               color_by = "part")
plot_bootstrap(ca_so, 
               target_id = "XANPAGTX0501_002104-T1", 
               units = "est_counts", 
               color_by = "part")

  • Of the 118 upregulated in apothecia, 87 have no functional annotations
  • 9 are secreted
ap_ca_genes<-ca_sig %>% filter(change=="apothecium") %>%
  left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
  select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
ap_ca_genes %>% 
  kable(format = "html", col.names = colnames(ap_ca_genes)) %>%
  kable_styling() %>%
  kableExtra::scroll_box(width = "100%", height = "600px")
target_id b InterPro_new CAZyme_new Protease_new KO secreted_consensus lichen_ortho
XANPAGTX0501_001605-T1 -1.002217 NA NA NA FALSE FALSE
XANPAGTX0501_004628-T1 -1.002890 IPR002156 Ribonuclease H domain, IPR012337 Ribonuclease H-like superfamily, IPR036397 Ribonuclease H superfamily NA NA K03469 FALSE FALSE
XANPAGTX0501_009621-T1 -1.004737 NA NA NA FALSE FALSE
XANPAGTX0501_008874-T1 -1.005597 NA NA NA FALSE TRUE
XANPAGTX0501_007403-T1 -1.005610 NA NA NA FALSE TRUE
XANPAGTX0501_004416-T1 -1.006355 IPR000246 Peptidase T2, asparaginase 2, IPR029055 Nucleophile aminohydrolases, N-terminal, IPR037464 Threonine aspartase 1 NA T02 K08657 FALSE FALSE
XANPAGTX0501_009141-T1 -1.008026 NA NA NA FALSE FALSE
XANPAGTX0501_002166-T1 -1.010246 NA NA NA FALSE FALSE
XANPAGTX0501_003282-T1 -1.010415 NA NA NA FALSE FALSE
XANPAGTX0501_006245-T1 -1.011007 NA NA NA TRUE TRUE
XANPAGTX0501_001082-T1 -1.011584 IPR004853 Sugar phosphate transporter domain NA NA K26222 FALSE FALSE
XANPAGTX0501_002170-T1 -1.014622 NA NA NA FALSE FALSE
XANPAGTX0501_002104-T1 -1.017319 NA NA NA FALSE FALSE
XANPAGTX0501_002183-T1 -1.017368 NA NA NA FALSE FALSE
XANPAGTX0501_004494-T1 -1.018387 NA NA NA FALSE FALSE
XANPAGTX0501_007464-T1 -1.021451 NA NA NA FALSE FALSE
XANPAGTX0501_005615-T1 -1.022220 NA NA NA FALSE FALSE
XANPAGTX0501_001888-T1 -1.023478 NA NA NA FALSE FALSE
XANPAGTX0501_005658-T1 -1.031831 IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily NA NA FALSE FALSE
XANPAGTX0501_002163-T1 -1.035184 NA NA NA FALSE FALSE
XANPAGTX0501_008533-T1 -1.037400 NA NA NA FALSE FALSE
XANPAGTX0501_009317-T1 -1.039048 IPR008979 Galactose-binding-like domain superfamily NA NA TRUE FALSE
XANPAGTX0501_005061-T1 -1.045582 NA NA NA TRUE FALSE
XANPAGTX0501_001947-T1 -1.046488 NA NA NA FALSE FALSE
XANPAGTX0501_004580-T1 -1.050842 IPR007292 Nuclear fusion protein Kar5 NA NA FALSE FALSE
XANPAGTX0501_006974-T1 -1.052396 NA NA NA FALSE FALSE
XANPAGTX0501_002057-T1 -1.052723 NA NA NA FALSE FALSE
XANPAGTX0501_006203-T1 -1.055462 IPR001841 Zinc finger, RING-type, IPR002867 IBR domain, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site NA NA FALSE FALSE
XANPAGTX0501_002184-T1 -1.055941 NA NA NA FALSE FALSE
XANPAGTX0501_001330-T1 -1.062267 NA NA NA FALSE TRUE
XANPAGTX0501_004493-T1 -1.069215 NA NA NA FALSE FALSE
XANPAGTX0501_005597-T1 -1.070417 IPR006421 Glycogen debranching enzyme, metazoa, IPR008928 Six-hairpin glycosidase superfamily, IPR012341 Six-hairpin glycosidase-like superfamily, IPR017853 Glycoside hydrolase superfamily, IPR029436 Eukaryotic glycogen debranching enzyme, N-terminal domain, IPR032788 Glycogen debranching enzyme, central domain, IPR032790 Glycogen debranching enzyme, C-terminal, IPR032792 Glycogen debranching enzyme, glucanotransferase domain GH133 NA K01196 FALSE FALSE
XANPAGTX0501_008628-T1 -1.071911 IPR023346 Lysozyme-like domain superfamily NA NA FALSE TRUE
XANPAGTX0501_003775-T1 -1.074091 IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily NA NA K11593 FALSE FALSE
XANPAGTX0501_000647-T1 -1.082215 IPR000571 Zinc finger, CCCH-type NA NA FALSE FALSE
XANPAGTX0501_006255-T1 -1.084624 NA NA NA FALSE FALSE
XANPAGTX0501_010303-T1 -1.086556 NA NA NA FALSE FALSE
XANPAGTX0501_004891-T1 -1.088838 NA NA NA FALSE FALSE
XANPAGTX0501_000681-T1 -1.089087 NA NA NA FALSE FALSE
XANPAGTX0501_001010-T1 -1.089790 NA NA NA FALSE FALSE
XANPAGTX0501_004217-T1 -1.090288 IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily NA NA K24990 FALSE FALSE
XANPAGTX0501_001436-T1 -1.091349 IPR002048 EF-hand domain, IPR011992 EF-hand domain pair, IPR018247 EF-Hand 1, calcium-binding site NA NA FALSE FALSE
XANPAGTX0501_006910-T1 -1.092752 NA NA NA FALSE FALSE
XANPAGTX0501_007871-T1 -1.093262 NA NA NA FALSE TRUE
XANPAGTX0501_000005-T1 -1.100476 NA NA NA FALSE FALSE
XANPAGTX0501_009139-T1 -1.106326 IPR001876 Zinc finger, RanBP2-type NA NA FALSE FALSE
XANPAGTX0501_001333-T1 -1.109653 NA NA NA FALSE TRUE
XANPAGTX0501_003212-T1 -1.110801 IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily NA NA FALSE TRUE
XANPAGTX0501_008009-T1 -1.110995 NA NA NA FALSE FALSE
XANPAGTX0501_006016-T1 -1.111020 IPR008928 Six-hairpin glycosidase superfamily, IPR031335 Glycosyl hydrolase family 63, C-terminal GH63 NA FALSE FALSE
XANPAGTX0501_008008-T1 -1.111120 NA NA NA FALSE FALSE
XANPAGTX0501_006330-T1 -1.113100 NA NA NA FALSE FALSE
XANPAGTX0501_004104-T1 -1.113445 IPR001214 SET domain, IPR011990 Tetratricopeptide-like helical domain superfamily NA NA FALSE FALSE
XANPAGTX0501_001362-T1 -1.113981 NA NA NA FALSE FALSE
XANPAGTX0501_001951-T1 -1.118810 NA NA NA FALSE FALSE
XANPAGTX0501_005630-T1 -1.120143 IPR036928 Amidase signature (AS) superfamily NA NA FALSE FALSE
XANPAGTX0501_008534-T1 -1.122508 NA NA NA FALSE FALSE
XANPAGTX0501_000025-T1 -1.123779 NA NA NA FALSE TRUE
XANPAGTX0501_004950-T1 -1.124212 NA NA NA FALSE FALSE
XANPAGTX0501_002522-T1 -1.132906 NA NA NA FALSE FALSE
XANPAGTX0501_003572-T1 -1.135075 IPR001087 GDSL lipase/esterase, IPR036514 SGNH hydrolase superfamily CE16 NA TRUE FALSE
XANPAGTX0501_007067-T1 -1.135736 NA NA NA FALSE TRUE
XANPAGTX0501_007234-T1 -1.142869 NA NA NA FALSE FALSE
XANPAGTX0501_007262-T1 -1.143084 NA NA NA FALSE TRUE
XANPAGTX0501_010203-T1 -1.143084 NA NA NA FALSE TRUE
XANPAGTX0501_005279-T1 -1.148052 NA NA NA FALSE FALSE
XANPAGTX0501_010380-T1 -1.148975 IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily NA NA FALSE TRUE
XANPAGTX0501_010007-T1 -1.149075 NA NA NA FALSE FALSE
XANPAGTX0501_009615-T1 -1.156978 IPR035940 CAP superfamily NA NA TRUE FALSE
XANPAGTX0501_002172-T1 -1.161670 NA NA NA FALSE FALSE
XANPAGTX0501_003209-T1 -1.170208 NA NA NA FALSE FALSE
XANPAGTX0501_008041-T1 -1.181328 NA NA NA TRUE FALSE
XANPAGTX0501_001910-T1 -1.190522 NA NA NA FALSE FALSE
XANPAGTX0501_009318-T1 -1.192876 IPR011333 SKP1/BTB/POZ domain superfamily NA NA FALSE FALSE
XANPAGTX0501_004521-T1 -1.198724 IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily NA NA FALSE FALSE
XANPAGTX0501_001612-T1 -1.207043 NA NA NA FALSE FALSE
XANPAGTX0501_010304-T1 -1.207964 NA NA NA FALSE FALSE
XANPAGTX0501_001538-T1 -1.211841 NA NA NA FALSE FALSE
XANPAGTX0501_009602-T1 -1.212068 NA NA NA FALSE FALSE
XANPAGTX0501_008007-T1 -1.213991 NA NA NA FALSE FALSE
XANPAGTX0501_008782-T1 -1.216240 NA NA NA FALSE FALSE
XANPAGTX0501_006951-T1 -1.222177 NA NA NA FALSE FALSE
XANPAGTX0501_005402-T1 -1.225284 NA NA NA FALSE TRUE
XANPAGTX0501_001414-T1 -1.228686 NA NA NA FALSE FALSE
XANPAGTX0501_000194-T1 -1.233329 IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR013780 Glycosyl hydrolase, all-beta, IPR017853 Glycoside hydrolase superfamily GH13 NA K01176 FALSE FALSE
XANPAGTX0501_005766-T1 -1.254576 NA NA NA FALSE FALSE
XANPAGTX0501_009582-T1 -1.264645 NA NA NA FALSE FALSE
XANPAGTX0501_005735-T1 -1.281286 IPR018824 Conidiation-specific protein 6 NA NA FALSE FALSE
XANPAGTX0501_008331-T1 -1.288651 NA NA NA FALSE FALSE
XANPAGTX0501_001611-T1 -1.298257 NA NA NA FALSE FALSE
XANPAGTX0501_007900-T1 -1.308741 NA NA NA FALSE TRUE
XANPAGTX0501_008090-T1 -1.312749 NA NA NA FALSE FALSE
XANPAGTX0501_002182-T1 -1.314625 NA NA NA FALSE FALSE
XANPAGTX0501_009619-T1 -1.314627 NA NA NA FALSE FALSE
XANPAGTX0501_008284-T1 -1.314835 IPR029044 Nucleotide-diphospho-sugar transferases GT2_Glyco_tranf_2 NA FALSE FALSE
XANPAGTX0501_004520-T1 -1.321604 NA NA NA FALSE FALSE
XANPAGTX0501_001963-T1 -1.324243 NA NA NA FALSE FALSE
XANPAGTX0501_001960-T1 -1.329881 NA NA NA FALSE FALSE
XANPAGTX0501_000193-T1 -1.344509 IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR017853 Glycoside hydrolase superfamily GH13 NA FALSE FALSE
XANPAGTX0501_001967-T1 -1.356557 NA NA NA FALSE FALSE
XANPAGTX0501_001063-T1 -1.359981 NA NA NA TRUE FALSE
XANPAGTX0501_001856-T1 -1.377390 IPR037176 Osmotin/thaumatin-like superfamily NA NA TRUE TRUE
XANPAGTX0501_002506-T1 -1.384452 NA NA NA FALSE FALSE
XANPAGTX0501_006327-T1 -1.392539 IPR018466 Yeast cell wall synthesis Kre9/Knh1-like, N-terminal NA NA TRUE FALSE
XANPAGTX0501_007397-T1 -1.396019 NA NA NA FALSE FALSE
XANPAGTX0501_007872-T1 -1.413947 NA NA NA FALSE TRUE
XANPAGTX0501_010596-T1 -1.414271 NA NA NA FALSE FALSE
XANPAGTX0501_008420-T1 -1.415724 NA NA NA FALSE FALSE
XANPAGTX0501_000892-T1 -1.427350 NA NA NA FALSE FALSE
XANPAGTX0501_000378-T1 -1.444983 NA NA NA FALSE FALSE
XANPAGTX0501_003211-T1 -1.502300 NA NA NA FALSE FALSE
XANPAGTX0501_010280-T1 -1.533833 NA NA NA FALSE FALSE
XANPAGTX0501_005814-T1 -1.541250 NA NA NA FALSE FALSE
XANPAGTX0501_009786-T1 -1.554050 NA NA NA FALSE FALSE
XANPAGTX0501_009926-T1 -1.646262 NA NA NA FALSE FALSE
XANPAGTX0501_004966-T1 -1.664164 NA NA NA FALSE FALSE
XANPAGTX0501_008109-T1 -2.657633 IPR004143 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain NA NA K03800 FALSE FALSE
XANPAGTX0501_001156-T3 -3.910405 IPR003822 Paired amphipathic helix, IPR013194 Histone deacetylase interacting domain, IPR031693 Sin3, C-terminal, IPR036600 Paired amphipathic helix superfamily NA NA K11644 FALSE FALSE
  • Selected only genes that are potentially multicellularity related
mult_list<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/multicellularity.txt")
#select genes that come from one of the categories of interest
ips_df <-funannot2 %>% select(TranscriptID,InterPro_new) %>% 
  mutate(InterPro_new = strsplit(InterPro_new, ", I")) %>%
        unnest(InterPro_new) %>% mutate(InterPro_new=str_replace(InterPro_new,"^PR","IPR")) %>%
  mutate(short_term = substr(InterPro_new, 1,40))

ips_selected<-ips_df %>% mutate(ID=gsub( " .*$", "", InterPro_new)) %>% inner_join(mult_list,relationship = "many-to-many") %>% select(-c(InterPro_new,short_term))
## Joining with `by = join_by(ID)`
ko_cazy_selected<-funannot2 %>% select(TranscriptID,KO,CAZyme_new) %>% 
  pivot_longer(-TranscriptID,names_to = "Annotation",values_to = "ID") %>% inner_join(mult_list,relationship = "many-to-many") %>% select(-Annotation)
## Joining with `by = join_by(ID)`
mult_gene_table<-rbind(ips_selected,ko_cazy_selected)  

mult_gene_table_ap<-mult_gene_table %>% inner_join(ca_sig %>% filter(change=="apothecium") %>% select(target_id,b),by=c("TranscriptID"="target_id")) %>% arrange(Function)

mult_gene_table_ap %>% 
  kable(format = "html", col.names = colnames(mult_gene_table_ap)) %>%
  kable_styling() %>%
  kableExtra::scroll_box(width = "100%", height = "600px")
TranscriptID ID Annotation_type Description Function Function_type b
XANPAGTX0501_005597-T1 IPR032788 IPR Glycogen debranching enzyme, central domain Carbohydrate storage Fungal multicellularity -1.070417
XANPAGTX0501_000647-T1 IPR000571 IPR Zinc finger, CCCH-type Cell division, proliferation and growth Fungal multicellularity -1.082215
XANPAGTX0501_003775-T1 IPR012337 IPR Ribonuclease H-like superfamily Cell division, proliferation and growth Fungal multicellularity -1.074091
XANPAGTX0501_004104-T1 IPR001214 IPR SET domain Cell division, proliferation and growth Fungal multicellularity -1.113445
XANPAGTX0501_004628-T1 IPR012337 IPR Ribonuclease H-like superfamily Cell division, proliferation and growth Fungal multicellularity -1.002890
XANPAGTX0501_005735-T1 IPR018824 IPR Conidiation-specific protein 6 Cell surface and cell wall proteins Fungal multicellularity -1.281286
XANPAGTX0501_006327-T1 IPR018466 IPR Yeast cell wall synthesis Kre9/Knh1-like, N-terminal Cell wall biosynthesis Fungal multicellularity -1.392539
XANPAGTX0501_001856-T1 IPR037176 IPR Osmotin/thaumatin-like superfamily Cell wall remodeling Fungal multicellularity -1.377390
XANPAGTX0501_003212-T1 IPR001810 IPR F-box domain Protein ubiquitination Fungal multicellularity -1.110801
XANPAGTX0501_006203-T1 IPR017907 IPR Zinc finger; RING-type; conserved site Protein ubiquitination Fungal multicellularity -1.055462
XANPAGTX0501_010380-T1 IPR000210 IPR BTB/POZ domain Protein ubiquitination Fungal multicellularity -1.148975
XANPAGTX0501_004217-T1 IPR000504 IPR RNA recognition motif domain RNA binding proteins Expression regulation -1.090288
XANPAGTX0501_003775-T1 IPR032474 IPR Protein argonaute, N-terminal RNA interference Expression regulation -1.074091
XANPAGTX0501_006203-T1 IPR013083 IPR Zinc finger, RING/FYVE/PHD-type Transcription factors Expression regulation -1.055462
  • Other notable proteins:
    • Another protein from ubiquitin degrading system with a F-box and LRR domains
    • Multiple transcription factors with different Zinc finger domains and IPR000210 BTB/POZ domain
    • IPR031693 Sin3, C-terminal, which is a transcriptional repressor
    • IPR018824 Conidiation-specific protein 6, function unknown
    • Secreted IPR035940 CAP superfamily protein (egulation of extracellular matrix and branching morphogenesis, either proteases or protease inhibitors)
    • Several GHs
  • InterPro enrichement analysis
###make table with IPS annotations
ips_df <-funannot2 %>% select(TranscriptID,InterPro_new) %>% 
  mutate(InterPro_new = strsplit(InterPro_new, ", I")) %>%
        unnest(InterPro_new) %>% mutate(InterPro_new=str_replace(InterPro_new,"^PR","IPR")) %>%
  mutate(short_term = substr(InterPro_new, 1,40))

ips_data <- list(
    term2protein = data.frame(
                        term = ips_df$InterPro_new,
                        gene = ips_df$TranscriptID
                        ),
    term2name = data.frame(
                        term = ips_df$InterPro_new,
                        name = ips_df$short_term
                        ),
    
    universe = unique(as.character(ips_df$TranscriptID))
)

###enrichment analysis
enrich<-clusterProfiler::enricher(ap_ca_genes$target_id,
    pAdjustMethod = "none",
    minGSSize = 1,
    maxGSSize = 2000,
    qvalueCutoff = 1,
    universe=ips_data$universe,
    TERM2GENE=ips_data$term2protein,
    TERM2NAME=ips_data$term2name)

enrich_pairwise<-enrichplot::pairwise_termsim(enrich)
enrichplot::emapplot(enrich_pairwise)

The only gene showed as upregulated in center.

  • This gene is expressed in most samples, but there is a high level of heterogeneity across different lichen individuals, obscuring the pattern of it being more highly expressed in the center
plot_bootstrap(ca_so, 
               target_id = ca_sig$target_id[which.max(ca_sig$b)], 
               units = "est_counts", 
               color_by = "part")

  • This is the second, which is just below the threshold (b = 0.98)
plot_bootstrap(ca_so, 
               target_id = "XANPAGTX0501_004633-T1", 
               units = "est_counts", 
               color_by = "part")

  • Nothing is known about either!
ce_ca_genes<-ca_sig %>% filter(b>0.9) %>%
  left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
  select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
ce_ca_genes %>% 
  kable(format = "html", col.names = colnames(ce_ca_genes)) %>%
  kable_styling() %>%
  kableExtra::scroll_box(width = "100%", height = "600px")
target_id b InterPro_new CAZyme_new Protease_new KO secreted_consensus lichen_ortho
XANPAGTX0501_006303-T1 1.3084877 NA NA NA FALSE TRUE
XANPAGTX0501_004633-T1 0.9765075 NA NA NA FALSE FALSE

3.2. Power analysis: simple

  • Do we have enough samples for this comparison?
  • Looked at the distribution of corrected p-values (a.k.a. q-values). The graph looks good: close to uniform, with an increase close to 0. If our test was underpowered, we would see an increase of p-vlaues along 0->1, but this is not the case
ggplot(ca_table)+geom_histogram(aes(x=qval))
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 690798 rows containing non-finite values (`stat_bin()`).

  • QQ-plot looks fine
library(MKpower)
qqunif(ca_table$qval, color.line = "orange")

4. Edge / apothetia comparison

ea_dirs<-kal_dirs2 %>% filter(part %in% c("thallus_edge", "apothecia") )
ea_dirs$part <- as.factor(ea_dirs$part)
ea_dirs$thallus<- as.factor(ea_dirs$thallus)

rhdf5::h5closeAll()
ea_so <- sleuth_prep(ea_dirs,extra_bootstrap_summary = TRUE,filter_target_id = target_id,transformation_function = function(x) log2(x + 0.1))
## Warning in check_num_cores(num_cores): It appears that you are running Sleuth from within Rstudio.
## Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
## If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
## reading in kallisto results
## dropping unused factor levels
## ...........
## normalizing est_counts
## A list of target IDs for filtering was found. Using this for filtering
## 11083 targets passed the filter
## normalizing tpm
## merging in metadata
## summarizing bootstraps
## ...........
#model that includes only confounding variables
ea_so <- sleuth_fit(ea_so, ~thallus, 'reduced') 
## fitting measurement error models
## shrinkage estimation
## computing variance of betas
#model that includes only both the confounding variable and the variable of interest
ea_so  <- sleuth_fit(ea_so, ~ thallus + part, 'full')
## fitting measurement error models
## shrinkage estimation
## 1 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_010086-T1
## computing variance of betas
#compare the models
ea_so <- sleuth_lrt(ea_so, 'reduced', 'full')
ea_so <- sleuth_wt(ea_so, 'partthallus_edge')

ea_table <- sleuth_results(ea_so, 'partthallus_edge')
ea_sig <- ea_table %>% tibble::as_tibble() %>% 
  filter( qval <= 0.05, grepl("GTX0501",target_id) ) %>% 
  arrange(desc(b)) %>% mutate(change = if_else(b > 1, "edge", ifelse(b< -1, "apothecium", "low_logFC")))

plot_pca(ea_so, color_by = 'part', text_labels = TRUE,use_filtered=T)

table(ea_sig$change)
## 
## apothecium       edge  low_logFC 
##        371         13       1772

Upregulated in apothecia

  • Bootstrap of the two genes most overexpressed in the apothecium.
plot_bootstrap(ea_so, 
               target_id = ea_sig$target_id[which.min(ea_sig$b)], 
               units = "est_counts", 
               color_by = "part")
plot_bootstrap(ea_so, 
               target_id = ea_sig$target_id[which.min(ea_sig$b[-which.min(ea_sig$b)])], 
               units = "est_counts", 
               color_by = "part")

  • Both MAT genes seem upregulated, with b-value of -1.8
plot_bootstrap(ea_so, 
               target_id = "XANPAGTX0501_002103-T1", 
               units = "est_counts", 
               color_by = "part")
plot_bootstrap(ea_so, 
               target_id = "XANPAGTX0501_002104-T1", 
               units = "est_counts", 
               color_by = "part")

  • Of the 371 upregulated in apothecia, 255 have no functional annotations
  • 33 are secreted
ap_ea_genes<-ea_sig %>% filter(change=="apothecium") %>%
  left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
  select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
ap_ea_genes %>% 
  kable(format = "html", col.names = colnames(ap_ea_genes)) %>%
  kable_styling() %>%
  kableExtra::scroll_box(width = "100%", height = "600px")
target_id b InterPro_new CAZyme_new Protease_new KO secreted_consensus lichen_ortho
XANPAGTX0501_006767-T1 -1.001121 IPR017956 AT hook, DNA-binding motif NA NA FALSE FALSE
XANPAGTX0501_001647-T1 -1.003441 NA NA NA FALSE FALSE
XANPAGTX0501_006026-T1 -1.005997 NA NA NA FALSE FALSE
XANPAGTX0501_010639-T1 -1.009995 NA NA NA FALSE TRUE
XANPAGTX0501_000350-T1 -1.010205 IPR003439 ABC transporter-like, ATP-binding domain, IPR003593 AAA+ ATPase domain, IPR013525 ABC-2 type transporter, IPR017871 ABC transporter-like, conserved site, IPR027417 P-loop containing nucleoside triphosphate hydrolase NA NA K05681 FALSE FALSE
XANPAGTX0501_005347-T1 -1.010680 NA NA NA FALSE FALSE
XANPAGTX0501_004759-T1 -1.011221 NA NA NA FALSE FALSE
XANPAGTX0501_006900-T1 -1.012780 NA NA NA FALSE FALSE
XANPAGTX0501_009389-T1 -1.014539 NA NA NA FALSE FALSE
XANPAGTX0501_007378-T1 -1.016970 NA NA NA FALSE FALSE
XANPAGTX0501_005621-T1 -1.020780 NA NA NA FALSE FALSE
XANPAGTX0501_010022-T1 -1.023610 NA NA NA TRUE FALSE
XANPAGTX0501_009499-T1 -1.023663 NA NA NA FALSE FALSE
XANPAGTX0501_006945-T1 -1.030462 NA NA NA FALSE FALSE
XANPAGTX0501_000661-T1 -1.032709 NA NA NA FALSE TRUE
XANPAGTX0501_006946-T1 -1.037233 NA NA NA FALSE FALSE
XANPAGTX0501_002624-T1 -1.038299 IPR029058 Alpha/Beta hydrolase fold NA NA FALSE FALSE
XANPAGTX0501_010094-T1 -1.039693 NA NA NA FALSE FALSE
XANPAGTX0501_008594-T1 -1.040188 IPR036259 MFS transporter superfamily NA NA FALSE FALSE
XANPAGTX0501_001497-T1 -1.040517 NA NA NA FALSE FALSE
XANPAGTX0501_000203-T1 -1.040557 IPR001938 Thaumatin family, IPR037176 Osmotin/thaumatin-like superfamily GH152 NA TRUE FALSE
XANPAGTX0501_010087-T1 -1.040935 NA NA NA FALSE FALSE
XANPAGTX0501_003186-T1 -1.041709 NA NA NA TRUE FALSE
XANPAGTX0501_010640-T1 -1.042747 NA NA NA FALSE FALSE
XANPAGTX0501_004003-T1 -1.043412 NA NA NA FALSE FALSE
XANPAGTX0501_000909-T1 -1.050406 NA NA NA FALSE FALSE
XANPAGTX0501_002181-T1 -1.050504 NA NA NA FALSE FALSE
XANPAGTX0501_010204-T1 -1.051517 NA NA NA FALSE TRUE
XANPAGTX0501_006142-T1 -1.056449 NA NA NA TRUE TRUE
XANPAGTX0501_005447-T1 -1.060382 IPR024500 Domain of unknown function DUF3074 NA NA FALSE FALSE
XANPAGTX0501_004484-T1 -1.063011 NA NA NA FALSE TRUE
XANPAGTX0501_000065-T1 -1.064314 IPR027921 NOP protein chaperone 1 NA NA FALSE FALSE
XANPAGTX0501_006920-T1 -1.066060 NA NA NA FALSE FALSE
XANPAGTX0501_003265-T1 -1.067945 IPR007203 ORMDL family NA NA FALSE FALSE
XANPAGTX0501_002152-T1 -1.069475 IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR040632 Sulfotransferase, S. mansonii-type NA NA FALSE TRUE
XANPAGTX0501_003742-T1 -1.069824 IPR001509 NAD-dependent epimerase/dehydratase, IPR036291 NAD(P)-binding domain superfamily NA NA FALSE FALSE
XANPAGTX0501_006931-T1 -1.072494 IPR013087 Zinc finger C2H2-type NA NA FALSE FALSE
XANPAGTX0501_002657-T1 -1.073491 NA NA NA FALSE FALSE
XANPAGTX0501_005924-T1 -1.074455 NA NA NA FALSE FALSE
XANPAGTX0501_007353-T1 -1.077217 NA NA NA FALSE TRUE
XANPAGTX0501_005583-T1 -1.079779 NA NA NA FALSE FALSE
XANPAGTX0501_009580-T1 -1.091993 NA NA NA FALSE FALSE
XANPAGTX0501_004141-T1 -1.102317 NA NA NA FALSE FALSE
XANPAGTX0501_010231-T1 -1.104490 NA NA NA FALSE FALSE
XANPAGTX0501_008637-T1 -1.106264 NA NA NA TRUE FALSE
XANPAGTX0501_000885-T1 -1.108859 IPR036305 RGS domain superfamily NA NA FALSE FALSE
XANPAGTX0501_003865-T1 -1.109235 NA NA NA TRUE FALSE
XANPAGTX0501_000417-T1 -1.109737 NA NA NA FALSE FALSE
XANPAGTX0501_005025-T1 -1.115496 NA NA NA FALSE FALSE
XANPAGTX0501_000848-T1 -1.115545 IPR016137 RGS domain, IPR036305 RGS domain superfamily NA NA FALSE TRUE
XANPAGTX0501_006384-T1 -1.125655 NA NA NA FALSE FALSE
XANPAGTX0501_004308-T1 -1.127582 NA NA NA FALSE FALSE
XANPAGTX0501_010011-T1 -1.134493 IPR036013 Band 7/SPFH domain superfamily NA NA K07192 FALSE FALSE
XANPAGTX0501_005047-T1 -1.135514 NA NA NA FALSE FALSE
XANPAGTX0501_002639-T1 -1.136570 IPR002740 EVE domain, IPR015947 PUA-like superfamily NA NA FALSE FALSE
XANPAGTX0501_006342-T1 -1.138964 NA NA NA FALSE TRUE
XANPAGTX0501_004244-T1 -1.139706 IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily NA NA FALSE FALSE
XANPAGTX0501_005153-T1 -1.141212 NA NA NA FALSE FALSE
XANPAGTX0501_009787-T1 -1.141882 NA NA NA FALSE FALSE
XANPAGTX0501_008527-T1 -1.142627 NA NA NA FALSE FALSE
XANPAGTX0501_009812-T1 -1.143459 NA NA NA FALSE FALSE
XANPAGTX0501_006215-T1 -1.145166 NA NA NA FALSE FALSE
XANPAGTX0501_001925-T1 -1.145918 IPR001841 Zinc finger, RING-type, IPR002867 IBR domain NA NA FALSE FALSE
XANPAGTX0501_006992-T1 -1.146775 NA NA NA FALSE FALSE
XANPAGTX0501_010010-T1 -1.146789 IPR036013 Band 7/SPFH domain superfamily NA NA FALSE FALSE
XANPAGTX0501_009594-T1 -1.149357 IPR002877 Ribosomal RNA methyltransferase, FtsJ domain, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily NA NA FALSE FALSE
XANPAGTX0501_005832-T1 -1.150654 IPR009836 Glycine-rich domain-containing protein-like NA NA FALSE FALSE
XANPAGTX0501_006250-T1 -1.153982 NA NA NA FALSE FALSE
XANPAGTX0501_002478-T1 -1.154555 IPR013126 Heat shock protein 70 family, IPR043129 ATPase, nucleotide binding domain NA NA FALSE FALSE
XANPAGTX0501_003033-T1 -1.155116 NA NA NA FALSE FALSE
XANPAGTX0501_002477-T1 -1.157099 NA NA NA FALSE FALSE
XANPAGTX0501_010530-T1 -1.158664 NA NA NA FALSE FALSE
XANPAGTX0501_001222-T1 -1.167774 NA NA NA FALSE FALSE
XANPAGTX0501_009738-T1 -1.170585 IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily NA NA FALSE TRUE
XANPAGTX0501_006766-T1 -1.171555 NA NA NA FALSE FALSE
XANPAGTX0501_010007-T1 -1.175289 NA NA NA FALSE FALSE
XANPAGTX0501_009438-T1 -1.175488 NA NA NA FALSE FALSE
XANPAGTX0501_003238-T1 -1.177022 NA NA NA FALSE FALSE
XANPAGTX0501_009437-T1 -1.179555 NA NA NA FALSE FALSE
XANPAGTX0501_010368-T1 -1.180001 NA NA NA FALSE FALSE
XANPAGTX0501_001509-T1 -1.181146 NA NA NA FALSE FALSE
XANPAGTX0501_001462-T1 -1.182311 IPR008775 Phytanoyl-CoA dioxygenase-like NA NA FALSE TRUE
XANPAGTX0501_005177-T1 -1.185673 IPR001313 Pumilio RNA-binding repeat, IPR011989 Armadillo-like helical, IPR016024 Armadillo-type fold, IPR033133 Pumilio homology domain, IPR033712 Pumilio, RNA binding domain NA NA FALSE FALSE
XANPAGTX0501_001839-T1 -1.189988 NA NA NA FALSE FALSE
XANPAGTX0501_009785-T1 -1.191020 NA NA NA FALSE FALSE
XANPAGTX0501_007467-T1 -1.203546 IPR013830 SGNH hydrolase-type esterase domain, IPR036514 SGNH hydrolase superfamily CE3 NA TRUE FALSE
XANPAGTX0501_010638-T1 -1.203845 IPR003593 AAA+ ATPase domain, IPR003959 ATPase, AAA-type, core, IPR027417 P-loop containing nucleoside triphosphate hydrolase NA NA FALSE TRUE
XANPAGTX0501_008862-T1 -1.204663 NA NA NA FALSE FALSE
XANPAGTX0501_008420-T1 -1.205385 NA NA NA FALSE FALSE
XANPAGTX0501_010529-T1 -1.212807 NA NA NA FALSE TRUE
XANPAGTX0501_001648-T1 -1.214948 IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily NA NA FALSE FALSE
XANPAGTX0501_005677-T1 -1.220573 IPR004313 Acireductone dioxygenase ARD family, IPR011051 RmlC-like cupin domain superfamily, IPR014710 RmlC-like jelly roll fold, IPR027496 Acireductone dioxygenase, eukaryotes NA NA K08967 FALSE FALSE
XANPAGTX0501_005317-T1 -1.226163 NA NA NA TRUE FALSE
XANPAGTX0501_005370-T1 -1.231519 NA NA NA FALSE FALSE
XANPAGTX0501_000888-T1 -1.234664 NA NA NA FALSE FALSE
XANPAGTX0501_009407-T1 -1.241242 NA NA NA FALSE FALSE
XANPAGTX0501_009599-T1 -1.242828 NA NA NA FALSE FALSE
XANPAGTX0501_006143-T1 -1.243856 NA NA NA FALSE FALSE
XANPAGTX0501_000622-T1 -1.244489 NA NA NA FALSE FALSE
XANPAGTX0501_007851-T1 -1.245823 NA NA NA FALSE FALSE
XANPAGTX0501_001498-T1 -1.248272 IPR012340 Nucleic acid-binding, OB-fold NA NA FALSE FALSE
XANPAGTX0501_008005-T1 -1.251448 IPR001965 Zinc finger, PHD-type, IPR011011 Zinc finger, FYVE/PHD-type, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR019786 Zinc finger, PHD-type, conserved site, IPR019787 Zinc finger, PHD-finger NA NA FALSE FALSE
XANPAGTX0501_005952-T1 -1.253184 IPR032675 Leucine-rich repeat domain superfamily NA NA FALSE TRUE
XANPAGTX0501_000707-T1 -1.255320 NA NA NA FALSE FALSE
XANPAGTX0501_003775-T2 -1.260916 IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily NA NA K11593 FALSE FALSE
XANPAGTX0501_005280-T1 -1.264296 NA NA NA FALSE FALSE
XANPAGTX0501_003264-T1 -1.264968 IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily NA NA FALSE FALSE
XANPAGTX0501_008708-T1 -1.265455 NA NA NA FALSE FALSE
XANPAGTX0501_001062-T1 -1.268232 NA NA NA FALSE TRUE
XANPAGTX0501_006095-T1 -1.272978 NA NA NA FALSE FALSE
XANPAGTX0501_009628-T1 -1.276921 NA NA NA FALSE FALSE
XANPAGTX0501_004596-T1 -1.281428 NA NA NA FALSE FALSE
XANPAGTX0501_004753-T1 -1.281897 NA NA NA FALSE FALSE
XANPAGTX0501_000281-T1 -1.282182 IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily NA NA FALSE TRUE
XANPAGTX0501_003198-T1 -1.286713 IPR022085 Oxopyrrolidines biosynthesis cluster protein G NA NA FALSE TRUE
XANPAGTX0501_010276-T1 -1.289004 NA NA NA FALSE FALSE
XANPAGTX0501_010523-T1 -1.289004 NA NA NA FALSE FALSE
XANPAGTX0501_007934-T1 -1.291157 NA NA NA FALSE FALSE
XANPAGTX0501_002054-T1 -1.291837 NA NA NA FALSE TRUE
XANPAGTX0501_005550-T1 -1.294683 IPR001810 F-box domain, IPR036047 F-box-like domain superfamily NA NA FALSE FALSE
XANPAGTX0501_005188-T1 -1.298616 NA NA NA FALSE FALSE
XANPAGTX0501_004102-T1 -1.299115 IPR000420 Yeast PIR protein repeat NA NA K26550 TRUE FALSE
XANPAGTX0501_002019-T1 -1.299594 NA NA NA FALSE FALSE
XANPAGTX0501_010021-T1 -1.299618 NA NA NA TRUE FALSE
XANPAGTX0501_002159-T1 -1.301773 NA NA NA FALSE TRUE
XANPAGTX0501_002946-T1 -1.307564 NA NA NA FALSE TRUE
XANPAGTX0501_003790-T1 -1.311097 NA NA NA FALSE TRUE
XANPAGTX0501_002123-T1 -1.312729 IPR000504 RNA recognition motif domain, IPR007855 RNA-dependent RNA polymerase, eukaryotic-type, IPR035979 RNA-binding domain superfamily NA NA K11699 FALSE FALSE
XANPAGTX0501_000751-T1 -1.312812 NA NA NA FALSE FALSE
XANPAGTX0501_001644-T1 -1.313601 NA NA NA FALSE FALSE
XANPAGTX0501_007232-T1 -1.314325 NA NA NA FALSE FALSE
XANPAGTX0501_006139-T1 -1.315900 NA NA NA FALSE FALSE
XANPAGTX0501_001436-T1 -1.320276 IPR002048 EF-hand domain, IPR011992 EF-hand domain pair, IPR018247 EF-Hand 1, calcium-binding site NA NA FALSE FALSE
XANPAGTX0501_006420-T1 -1.320799 NA NA NA FALSE FALSE
XANPAGTX0501_005281-T1 -1.324225 NA NA NA FALSE FALSE
XANPAGTX0501_004466-T1 -1.328900 IPR000490 Glycoside hydrolase family 17, IPR017853 Glycoside hydrolase superfamily, IPR018620 Ubiquitin 3 binding protein But2, C-terminal NA NA TRUE FALSE
XANPAGTX0501_002098-T1 -1.334348 IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily NA NA FALSE FALSE
XANPAGTX0501_007833-T1 -1.343993 IPR002889 Carbohydrate-binding WSC, IPR018535 Domain of unknown function DUF1996 NA NA FALSE FALSE
XANPAGTX0501_004270-T1 -1.346903 IPR009465 Spondin, N-terminal NA NA FALSE FALSE
XANPAGTX0501_003124-T1 -1.348872 IPR001461 Aspartic peptidase A1 family, IPR001969 Aspartic peptidase, active site, IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain, IPR034164 Pepsin-like domain NA A01A TRUE FALSE
XANPAGTX0501_000938-T1 -1.358336 NA NA NA FALSE FALSE
XANPAGTX0501_007254-T1 -1.362647 NA NA NA FALSE FALSE
XANPAGTX0501_010211-T1 -1.362647 NA NA NA FALSE FALSE
XANPAGTX0501_008200-T1 -1.362879 NA NA NA FALSE FALSE
XANPAGTX0501_003864-T1 -1.363940 IPR009075 Acyl-CoA dehydrogenase/oxidase C-terminal, IPR009100 Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily, IPR013786 Acyl-CoA dehydrogenase/oxidase, N-terminal, IPR036250 Acyl-CoA dehydrogenase-like, C-terminal, IPR037069 Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily NA NA FALSE FALSE
XANPAGTX0501_005775-T1 -1.364250 NA NA NA FALSE FALSE
XANPAGTX0501_007473-T1 -1.375934 NA NA NA FALSE FALSE
XANPAGTX0501_007936-T1 -1.379176 NA NA NA FALSE FALSE
XANPAGTX0501_005640-T1 -1.380432 IPR013087 Zinc finger C2H2-type NA NA FALSE TRUE
XANPAGTX0501_000026-T1 -1.381814 NA NA NA FALSE FALSE
XANPAGTX0501_010180-T1 -1.383532 NA NA NA FALSE FALSE
XANPAGTX0501_010275-T1 -1.384204 IPR003593 AAA+ ATPase domain, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR041679 DNA2/NAM7 helicase-like, C-terminal NA NA FALSE TRUE
XANPAGTX0501_006203-T1 -1.386200 IPR001841 Zinc finger, RING-type, IPR002867 IBR domain, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site NA NA FALSE FALSE
XANPAGTX0501_001955-T1 -1.387192 IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain, IPR001451 Hexapeptide repeat, IPR002110 Ankyrin repeat, IPR011004 Trimeric LpxA-like superfamily, IPR018357 Hexapeptide transferase, conserved site, IPR020683 Domain of unknown function DUF3447, IPR024688 Maltose/galactoside acetyltransferase, IPR036770 Ankyrin repeat-containing domain superfamily, IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily NA NA FALSE FALSE
XANPAGTX0501_009761-T1 -1.387848 IPR001283 Cysteine-rich secretory protein-related, IPR014044 CAP domain, IPR018244 Allergen V5/Tpx-1-related, conserved site, IPR034120 None, IPR035940 CAP superfamily NA NA K20412 TRUE FALSE
XANPAGTX0501_002410-T1 -1.391729 NA NA NA FALSE FALSE
XANPAGTX0501_006114-T1 -1.393540 IPR001680 WD40 repeat, IPR015943 WD40/YVTN repeat-like-containing domain superfamily, IPR036322 WD40-repeat-containing domain superfamily NA NA K12782 FALSE FALSE
XANPAGTX0501_007365-T1 -1.397815 NA NA NA FALSE FALSE
XANPAGTX0501_009326-T1 -1.398307 NA NA NA FALSE FALSE
XANPAGTX0501_005584-T1 -1.398387 NA NA NA FALSE FALSE
XANPAGTX0501_001825-T1 -1.402807 IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily NA NA FALSE FALSE
XANPAGTX0501_010380-T1 -1.404538 IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily NA NA FALSE TRUE
XANPAGTX0501_000033-T1 -1.410231 IPR002656 Acyltransferase 3 domain NA NA FALSE FALSE
XANPAGTX0501_009293-T1 -1.419596 NA NA NA TRUE FALSE
XANPAGTX0501_004008-T1 -1.420375 NA NA NA FALSE FALSE
XANPAGTX0501_000036-T1 -1.420457 IPR006640 SprT-like NA NA FALSE FALSE
XANPAGTX0501_009581-T1 -1.427218 NA NA NA FALSE FALSE
XANPAGTX0501_008888-T1 -1.427796 IPR007527 Zinc finger, SWIM-type NA NA FALSE TRUE
XANPAGTX0501_003765-T1 -1.428029 IPR000420 Yeast PIR protein repeat NA NA TRUE FALSE
XANPAGTX0501_000697-T1 -1.443805 NA NA NA TRUE FALSE
XANPAGTX0501_006214-T1 -1.444244 NA NA NA FALSE TRUE
XANPAGTX0501_009795-T2 -1.444535 IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily NA NA FALSE FALSE
XANPAGTX0501_010304-T1 -1.458420 NA NA NA FALSE FALSE
XANPAGTX0501_006422-T1 -1.460727 NA NA NA FALSE FALSE
XANPAGTX0501_004978-T1 -1.460984 NA NA NA TRUE FALSE
XANPAGTX0501_009621-T1 -1.461288 NA NA NA FALSE FALSE
XANPAGTX0501_006909-T1 -1.464054 NA NA NA FALSE FALSE
XANPAGTX0501_008863-T1 -1.466559 NA NA NA FALSE FALSE
XANPAGTX0501_002007-T1 -1.467093 NA NA NA TRUE TRUE
XANPAGTX0501_002820-T1 -1.467192 NA NA NA FALSE TRUE
XANPAGTX0501_006246-T1 -1.468497 NA NA NA FALSE FALSE
XANPAGTX0501_007869-T1 -1.472330 IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily NA NA FALSE FALSE
XANPAGTX0501_005619-T1 -1.474796 NA NA NA FALSE FALSE
XANPAGTX0501_010379-T1 -1.475645 NA NA NA FALSE FALSE
XANPAGTX0501_008874-T1 -1.479109 NA NA NA FALSE TRUE
XANPAGTX0501_006459-T1 -1.480266 NA NA NA FALSE FALSE
XANPAGTX0501_009605-T1 -1.480669 NA NA NA FALSE FALSE
XANPAGTX0501_002963-T1 -1.487093 IPR000172 Glucose-methanol-choline oxidoreductase, N-terminal, IPR007867 Glucose-methanol-choline oxidoreductase, C-terminal, IPR012132 Glucose-methanol-choline oxidoreductase, IPR036188 FAD/NAD(P)-binding domain superfamily AA3 NA K00108 TRUE FALSE
XANPAGTX0501_009942-T1 -1.494661 IPR001810 F-box domain, IPR036047 F-box-like domain superfamily NA NA FALSE FALSE
XANPAGTX0501_001951-T1 -1.498238 NA NA NA FALSE FALSE
XANPAGTX0501_004853-T1 -1.500419 IPR000719 Protein kinase domain, IPR000961 AGC-kinase, C-terminal, IPR011009 Protein kinase-like domain superfamily NA NA FALSE FALSE
XANPAGTX0501_003361-T1 -1.505428 NA NA NA TRUE FALSE
XANPAGTX0501_001820-T2 -1.510192 IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain NA NA FALSE FALSE
XANPAGTX0501_000691-T1 -1.511934 NA NA NA FALSE TRUE
XANPAGTX0501_001710-T1 -1.512838 IPR007577 Glycosyltransferase, DXD sugar-binding motif, IPR029044 Nucleotide-diphospho-sugar transferases GT32 NA FALSE FALSE
XANPAGTX0501_003448-T1 -1.515924 NA NA NA TRUE TRUE
XANPAGTX0501_000420-T1 -1.518444 IPR013087 Zinc finger C2H2-type NA NA FALSE FALSE
XANPAGTX0501_005278-T1 -1.521181 NA NA NA FALSE FALSE
XANPAGTX0501_010051-T1 -1.529828 NA NA NA FALSE FALSE
XANPAGTX0501_000910-T1 -1.530331 NA NA NA FALSE FALSE
XANPAGTX0501_009511-T1 -1.533303 IPR000757 Glycoside hydrolase family 16, IPR001002 Chitin-binding, type 1, IPR008264 Beta-glucanase, IPR013320 Concanavalin A-like lectin/glucanase domain superfamily, IPR036861 Endochitinase-like superfamily GH16 NA K01216 TRUE FALSE
XANPAGTX0501_008533-T1 -1.540302 NA NA NA FALSE FALSE
XANPAGTX0501_009737-T1 -1.540774 IPR005829 Sugar transporter, conserved site, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily NA NA FALSE FALSE
XANPAGTX0501_009141-T1 -1.543886 NA NA NA FALSE FALSE
XANPAGTX0501_007899-T1 -1.544599 NA NA NA FALSE FALSE
XANPAGTX0501_003247-T1 -1.545289 IPR001878 Zinc finger, CCHC-type, IPR025836 Zinc knuckle CX2CX4HX4C, IPR036875 Zinc finger, CCHC-type superfamily NA NA K09250 FALSE FALSE
XANPAGTX0501_009666-T1 -1.554891 NA NA NA FALSE FALSE
XANPAGTX0501_001082-T1 -1.559541 IPR004853 Sugar phosphate transporter domain NA NA K26222 FALSE FALSE
XANPAGTX0501_005402-T1 -1.560177 NA NA NA FALSE TRUE
XANPAGTX0501_000872-T1 -1.562878 NA NA NA FALSE FALSE
XANPAGTX0501_005296-T1 -1.568716 IPR018750 Protein of unknown function DUF2306, membrane NA NA FALSE FALSE
XANPAGTX0501_004018-T2 -1.571979 IPR011009 Protein kinase-like domain superfamily, IPR016477 Fructosamine/Ketosamine-3-kinase NA NA FALSE TRUE
XANPAGTX0501_007750-T1 -1.577297 IPR027417 P-loop containing nucleoside triphosphate hydrolase NA NA FALSE FALSE
XANPAGTX0501_004416-T1 -1.578773 IPR000246 Peptidase T2, asparaginase 2, IPR029055 Nucleophile aminohydrolases, N-terminal, IPR037464 Threonine aspartase 1 NA T02 K08657 FALSE FALSE
XANPAGTX0501_007403-T1 -1.582309 NA NA NA FALSE TRUE
XANPAGTX0501_010598-T1 -1.582325 NA NA NA FALSE FALSE
XANPAGTX0501_009600-T1 -1.583776 NA NA NA FALSE FALSE
XANPAGTX0501_007231-T1 -1.583790 NA NA NA FALSE FALSE
XANPAGTX0501_010381-T1 -1.592206 IPR002293 Amino acid/polyamine transporter I NA NA K03294 FALSE FALSE
XANPAGTX0501_008534-T1 -1.593016 NA NA NA FALSE FALSE
XANPAGTX0501_001512-T1 -1.603338 NA NA NA FALSE FALSE
XANPAGTX0501_001061-T1 -1.603339 IPR002328 Alcohol dehydrogenase, zinc-type, conserved site, IPR011032 GroES-like superfamily, IPR013149 Alcohol dehydrogenase-like, C-terminal, IPR013154 Alcohol dehydrogenase-like, N-terminal, IPR020843 Polyketide synthase, enoylreductase domain, IPR036291 NAD(P)-binding domain superfamily NA NA FALSE FALSE
XANPAGTX0501_001953-T1 -1.607205 NA NA NA FALSE FALSE
XANPAGTX0501_005049-T1 -1.612235 NA NA NA FALSE FALSE
XANPAGTX0501_002057-T1 -1.616294 NA NA NA FALSE FALSE
XANPAGTX0501_008008-T1 -1.617050 NA NA NA FALSE FALSE
XANPAGTX0501_006330-T1 -1.618394 NA NA NA FALSE FALSE
XANPAGTX0501_001064-T1 -1.621988 IPR021765 Mycotoxin biosynthesis protein UstYa-like NA NA FALSE FALSE
XANPAGTX0501_009887-T1 -1.625740 NA NA NA TRUE FALSE
XANPAGTX0501_001965-T1 -1.632952 NA NA NA FALSE FALSE
XANPAGTX0501_008628-T1 -1.639869 IPR023346 Lysozyme-like domain superfamily NA NA FALSE TRUE
XANPAGTX0501_000025-T1 -1.641669 NA NA NA FALSE TRUE
XANPAGTX0501_001362-T1 -1.647839 NA NA NA FALSE FALSE
XANPAGTX0501_003283-T1 -1.648782 NA NA NA FALSE FALSE
XANPAGTX0501_001948-T1 -1.662753 NA NA NA FALSE FALSE
XANPAGTX0501_001888-T1 -1.678493 NA NA NA FALSE FALSE
XANPAGTX0501_001950-T1 -1.678963 NA NA NA FALSE FALSE
XANPAGTX0501_007464-T1 -1.685849 NA NA NA FALSE FALSE
XANPAGTX0501_002213-T1 -1.688746 IPR000629 ATP-dependent RNA helicase DEAD-box, conserved site, IPR001650 Helicase, C-terminal, IPR011545 DEAD/DEAH box helicase domain, IPR014001 Helicase superfamily 1/2, ATP-binding domain, IPR014014 RNA helicase, DEAD-box type, Q motif, IPR027417 P-loop containing nucleoside triphosphate hydrolase NA NA FALSE FALSE
XANPAGTX0501_009316-T1 -1.697722 IPR001810 F-box domain, IPR036047 F-box-like domain superfamily NA NA FALSE FALSE
XANPAGTX0501_009886-T1 -1.705744 NA NA NA TRUE FALSE
XANPAGTX0501_003282-T1 -1.706541 NA NA NA FALSE FALSE
XANPAGTX0501_008426-T1 -1.707030 NA NA NA FALSE FALSE
XANPAGTX0501_001330-T1 -1.707882 NA NA NA FALSE TRUE
XANPAGTX0501_000681-T1 -1.709567 NA NA NA FALSE FALSE
XANPAGTX0501_001964-T1 -1.727590 IPR001611 Leucine-rich repeat, IPR003591 Leucine-rich repeat, typical subtype, IPR019487 RAM signalling pathway, SOG2, IPR032675 Leucine-rich repeat domain superfamily NA NA FALSE FALSE
XANPAGTX0501_001949-T1 -1.732732 NA NA NA FALSE FALSE
XANPAGTX0501_006245-T1 -1.743213 NA NA NA TRUE TRUE
XANPAGTX0501_003212-T1 -1.757104 IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily NA NA FALSE TRUE
XANPAGTX0501_009317-T1 -1.758003 IPR008979 Galactose-binding-like domain superfamily NA NA TRUE FALSE
XANPAGTX0501_009582-T1 -1.765103 NA NA NA FALSE FALSE
XANPAGTX0501_004217-T1 -1.766312 IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily NA NA K24990 FALSE FALSE
XANPAGTX0501_005394-T1 -1.767362 IPR002575 Aminoglycoside phosphotransferase, IPR011009 Protein kinase-like domain superfamily NA NA FALSE FALSE
XANPAGTX0501_001947-T1 -1.767840 NA NA NA FALSE FALSE
XANPAGTX0501_003775-T1 -1.770114 IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily NA NA K11593 FALSE FALSE
XANPAGTX0501_008419-T1 -1.778819 NA NA NA FALSE FALSE
XANPAGTX0501_004950-T1 -1.782824 NA NA NA FALSE FALSE
XANPAGTX0501_002170-T1 -1.786506 NA NA NA FALSE FALSE
XANPAGTX0501_000893-T1 -1.791529 NA NA NA FALSE FALSE
XANPAGTX0501_004628-T1 -1.792127 IPR002156 Ribonuclease H domain, IPR012337 Ribonuclease H-like superfamily, IPR036397 Ribonuclease H superfamily NA NA K03469 FALSE FALSE
XANPAGTX0501_007343-T1 -1.792140 NA NA NA FALSE FALSE
XANPAGTX0501_004494-T1 -1.792536 NA NA NA FALSE FALSE
XANPAGTX0501_010117-T1 -1.793767 IPR002110 Ankyrin repeat, IPR011009 Protein kinase-like domain superfamily, IPR016477 Fructosamine/Ketosamine-3-kinase, IPR020683 Domain of unknown function DUF3447, IPR036770 Ankyrin repeat-containing domain superfamily NA NA K15523 FALSE FALSE
XANPAGTX0501_006449-T1 -1.796457 NA NA NA FALSE FALSE
XANPAGTX0501_000005-T1 -1.801160 NA NA NA FALSE FALSE
XANPAGTX0501_005658-T1 -1.801278 IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily NA NA FALSE FALSE
XANPAGTX0501_003213-T1 -1.804291 IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily NA NA FALSE TRUE
XANPAGTX0501_001954-T1 -1.808672 NA NA NA FALSE FALSE
XANPAGTX0501_004580-T1 -1.809609 IPR007292 Nuclear fusion protein Kar5 NA NA FALSE FALSE
XANPAGTX0501_002103-T1 -1.810531 IPR036910 High mobility group box domain superfamily NA NA FALSE FALSE
XANPAGTX0501_005597-T1 -1.816345 IPR006421 Glycogen debranching enzyme, metazoa, IPR008928 Six-hairpin glycosidase superfamily, IPR012341 Six-hairpin glycosidase-like superfamily, IPR017853 Glycoside hydrolase superfamily, IPR029436 Eukaryotic glycogen debranching enzyme, N-terminal domain, IPR032788 Glycogen debranching enzyme, central domain, IPR032790 Glycogen debranching enzyme, C-terminal, IPR032792 Glycogen debranching enzyme, glucanotransferase domain GH133 NA K01196 FALSE FALSE
XANPAGTX0501_005613-T1 -1.817996 IPR003615 HNH nuclease NA NA FALSE TRUE
XANPAGTX0501_006016-T1 -1.831989 IPR008928 Six-hairpin glycosidase superfamily, IPR031335 Glycosyl hydrolase family 63, C-terminal GH63 NA FALSE FALSE
XANPAGTX0501_002104-T1 -1.835003 NA NA NA FALSE FALSE
XANPAGTX0501_007067-T1 -1.839308 NA NA NA FALSE TRUE
XANPAGTX0501_001612-T1 -1.846971 NA NA NA FALSE FALSE
XANPAGTX0501_000398-T1 -1.847702 NA NA NA FALSE FALSE
XANPAGTX0501_004493-T1 -1.857771 NA NA NA FALSE FALSE
XANPAGTX0501_007244-T1 -1.858539 NA NA NA FALSE FALSE
XANPAGTX0501_000610-T1 -1.868687 NA NA NA FALSE FALSE
XANPAGTX0501_001333-T1 -1.870374 NA NA NA FALSE TRUE
XANPAGTX0501_009927-T1 -1.870484 NA NA NA FALSE TRUE
XANPAGTX0501_007870-T1 -1.874070 NA NA NA FALSE FALSE
XANPAGTX0501_004104-T1 -1.878122 IPR001214 SET domain, IPR011990 Tetratricopeptide-like helical domain superfamily NA NA FALSE FALSE
XANPAGTX0501_005631-T1 -1.885566 IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily NA NA FALSE FALSE
XANPAGTX0501_009786-T1 -1.894942 NA NA NA FALSE FALSE
XANPAGTX0501_002185-T1 -1.897085 NA NA NA FALSE FALSE
XANPAGTX0501_002163-T1 -1.904022 NA NA NA FALSE FALSE
XANPAGTX0501_006255-T1 -1.904541 NA NA NA FALSE FALSE
XANPAGTX0501_001643-T1 -1.910689 IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily NA NA FALSE TRUE
XANPAGTX0501_010222-T1 -1.912114 NA NA NA FALSE FALSE
XANPAGTX0501_002166-T1 -1.917720 NA NA NA FALSE FALSE
XANPAGTX0501_009926-T1 -1.919959 NA NA NA FALSE FALSE
XANPAGTX0501_000194-T1 -1.934433 IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR013780 Glycosyl hydrolase, all-beta, IPR017853 Glycoside hydrolase superfamily GH13 NA K01176 FALSE FALSE
XANPAGTX0501_000647-T1 -1.940161 IPR000571 Zinc finger, CCCH-type NA NA FALSE FALSE
XANPAGTX0501_001956-T1 -1.941094 NA NA NA FALSE FALSE
XANPAGTX0501_008090-T1 -1.954350 NA NA NA FALSE FALSE
XANPAGTX0501_002165-T1 -1.959472 NA NA NA FALSE FALSE
XANPAGTX0501_005620-T1 -1.973360 IPR001841 Zinc finger, RING-type, IPR004331 SPX domain, IPR011016 Zinc finger, RING-CH-type, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site NA NA FALSE TRUE
XANPAGTX0501_004520-T1 -1.985803 NA NA NA FALSE FALSE
XANPAGTX0501_001605-T1 -1.990522 NA NA NA FALSE FALSE
XANPAGTX0501_001538-T1 -1.994056 NA NA NA FALSE FALSE
XANPAGTX0501_001414-T1 -1.994528 NA NA NA FALSE FALSE
XANPAGTX0501_005048-T1 -1.997677 NA NA NA FALSE FALSE
XANPAGTX0501_000604-T1 -1.997943 NA NA NA FALSE FALSE
XANPAGTX0501_001958-T1 -1.998637 IPR001356 Homeobox domain, IPR009057 Homeobox-like domain superfamily, IPR017970 Homeobox, conserved site NA NA FALSE FALSE
XANPAGTX0501_006974-T1 -2.000740 NA NA NA FALSE FALSE
XANPAGTX0501_009615-T1 -2.000853 IPR035940 CAP superfamily NA NA TRUE FALSE
XANPAGTX0501_001952-T1 -2.002699 NA NA NA FALSE FALSE
XANPAGTX0501_008041-T1 -2.016189 NA NA NA TRUE FALSE
XANPAGTX0501_005630-T1 -2.027229 IPR036928 Amidase signature (AS) superfamily NA NA FALSE FALSE
XANPAGTX0501_002522-T1 -2.030035 NA NA NA FALSE FALSE
XANPAGTX0501_006910-T1 -2.032529 NA NA NA FALSE FALSE
XANPAGTX0501_001967-T1 -2.032808 NA NA NA FALSE FALSE
XANPAGTX0501_003572-T1 -2.044217 IPR001087 GDSL lipase/esterase, IPR036514 SGNH hydrolase superfamily CE16 NA TRUE FALSE
XANPAGTX0501_010303-T1 -2.054768 NA NA NA FALSE FALSE
XANPAGTX0501_005279-T1 -2.055973 NA NA NA FALSE FALSE
XANPAGTX0501_009139-T1 -2.056685 IPR001876 Zinc finger, RanBP2-type NA NA FALSE FALSE
XANPAGTX0501_004891-T1 -2.057500 NA NA NA FALSE FALSE
XANPAGTX0501_001910-T1 -2.062241 NA NA NA FALSE FALSE
XANPAGTX0501_007873-T1 -2.067522 NA NA NA FALSE TRUE
XANPAGTX0501_007871-T1 -2.081123 NA NA NA FALSE TRUE
XANPAGTX0501_005615-T1 -2.092197 NA NA NA FALSE FALSE
XANPAGTX0501_009318-T1 -2.097684 IPR011333 SKP1/BTB/POZ domain superfamily NA NA FALSE FALSE
XANPAGTX0501_005735-T1 -2.102015 IPR018824 Conidiation-specific protein 6 NA NA FALSE FALSE
XANPAGTX0501_007872-T1 -2.105800 NA NA NA FALSE TRUE
XANPAGTX0501_001611-T1 -2.125697 NA NA NA FALSE FALSE
XANPAGTX0501_005814-T1 -2.129685 NA NA NA FALSE FALSE
XANPAGTX0501_001859-T1 -2.142380 NA NA NA FALSE TRUE
XANPAGTX0501_007262-T1 -2.149005 NA NA NA FALSE TRUE
XANPAGTX0501_010203-T1 -2.149005 NA NA NA FALSE TRUE
XANPAGTX0501_008856-T1 -2.160218 IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily NA NA FALSE TRUE
XANPAGTX0501_005061-T1 -2.166875 NA NA NA TRUE FALSE
XANPAGTX0501_002183-T1 -2.174606 NA NA NA FALSE FALSE
XANPAGTX0501_002182-T1 -2.180402 NA NA NA FALSE FALSE
XANPAGTX0501_002763-T1 -2.184556 NA NA NA FALSE FALSE
XANPAGTX0501_009619-T1 -2.203533 NA NA NA FALSE FALSE
XANPAGTX0501_005766-T1 -2.223453 NA NA NA FALSE FALSE
XANPAGTX0501_004414-T1 -2.230880 IPR027417 P-loop containing nucleoside triphosphate hydrolase NA NA FALSE TRUE
XANPAGTX0501_006957-T1 -2.252415 NA NA NA FALSE FALSE
XANPAGTX0501_005614-T1 -2.252890 NA NA NA FALSE FALSE
XANPAGTX0501_001960-T1 -2.264721 NA NA NA FALSE FALSE
XANPAGTX0501_010596-T1 -2.271872 NA NA NA FALSE FALSE
XANPAGTX0501_000193-T1 -2.283992 IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR017853 Glycoside hydrolase superfamily GH13 NA FALSE FALSE
XANPAGTX0501_004521-T1 -2.284391 IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily NA NA FALSE FALSE
XANPAGTX0501_002172-T1 -2.285092 NA NA NA FALSE FALSE
XANPAGTX0501_008331-T1 -2.302060 NA NA NA FALSE FALSE
XANPAGTX0501_002184-T1 -2.304675 NA NA NA FALSE FALSE
XANPAGTX0501_004966-T1 -2.317059 NA NA NA FALSE FALSE
XANPAGTX0501_001959-T1 -2.362237 IPR000095 CRIB domain, IPR000719 Protein kinase domain, IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily, IPR017441 Protein kinase, ATP binding site, IPR033923 p21 activated kinase binding domain, IPR036936 CRIB domain superfamily NA NA FALSE FALSE
XANPAGTX0501_001063-T1 -2.369606 NA NA NA TRUE FALSE
XANPAGTX0501_008284-T1 -2.429045 IPR029044 Nucleotide-diphospho-sugar transferases GT2_Glyco_tranf_2 NA FALSE FALSE
XANPAGTX0501_008782-T1 -2.431407 NA NA NA FALSE FALSE
XANPAGTX0501_001966-T1 -2.436706 NA NA NA FALSE FALSE
XANPAGTX0501_003209-T1 -2.437600 NA NA NA FALSE FALSE
XANPAGTX0501_008009-T1 -2.444813 NA NA NA FALSE FALSE
XANPAGTX0501_001962-T1 -2.456164 NA NA NA FALSE FALSE
XANPAGTX0501_008007-T1 -2.479715 NA NA NA FALSE FALSE
XANPAGTX0501_007397-T1 -2.486783 NA NA NA FALSE FALSE
XANPAGTX0501_000378-T1 -2.490902 NA NA NA FALSE FALSE
XANPAGTX0501_009602-T1 -2.500879 NA NA NA FALSE FALSE
XANPAGTX0501_006951-T1 -2.507920 NA NA NA FALSE FALSE
XANPAGTX0501_002164-T1 -2.527734 NA NA NA FALSE FALSE
XANPAGTX0501_001856-T1 -2.592477 IPR037176 Osmotin/thaumatin-like superfamily NA NA TRUE TRUE
XANPAGTX0501_007900-T1 -2.636563 NA NA NA FALSE TRUE
XANPAGTX0501_006327-T1 -2.649849 IPR018466 Yeast cell wall synthesis Kre9/Knh1-like, N-terminal NA NA TRUE FALSE
XANPAGTX0501_002506-T1 -2.726475 NA NA NA FALSE FALSE
XANPAGTX0501_010050-T2 -2.757580 NA NA NA FALSE FALSE
XANPAGTX0501_003211-T1 -2.931999 NA NA NA FALSE FALSE
XANPAGTX0501_007239-T1 -3.420906 IPR027417 P-loop containing nucleoside triphosphate hydrolase NA NA FALSE FALSE
XANPAGTX0501_008519-T2 -4.617470 NA NA NA FALSE FALSE
  • Selected only genes that are potentially multicellularity related
mult_gene_table_ap2<-mult_gene_table %>% inner_join(ea_sig %>% filter(change=="apothecium") %>% select(target_id,b),by=c("TranscriptID"="target_id")) %>% arrange(Function)

mult_gene_table_ap2 %>% 
  kable(format = "html", col.names = colnames(mult_gene_table_ap2)) %>%
  kable_styling() %>%
  kableExtra::scroll_box(width = "100%", height = "600px")
TranscriptID ID Annotation_type Description Function Function_type b
XANPAGTX0501_001061-T1 IPR013149 IPR Alcohol dehydrogenase-like, C-terminal Acetyl-CoA production and metabolism Fungal multicellularity -1.603339
XANPAGTX0501_005597-T1 IPR032788 IPR Glycogen debranching enzyme, central domain Carbohydrate storage Fungal multicellularity -1.816345
XANPAGTX0501_000647-T1 IPR000571 IPR Zinc finger, CCCH-type Cell division, proliferation and growth Fungal multicellularity -1.940161
XANPAGTX0501_002213-T1 IPR001650 IPR Helicase, C-terminal Cell division, proliferation and growth Fungal multicellularity -1.688746
XANPAGTX0501_003775-T1 IPR012337 IPR Ribonuclease H-like superfamily Cell division, proliferation and growth Fungal multicellularity -1.770114
XANPAGTX0501_003775-T2 IPR012337 IPR Ribonuclease H-like superfamily Cell division, proliferation and growth Fungal multicellularity -1.260916
XANPAGTX0501_004104-T1 IPR001214 IPR SET domain Cell division, proliferation and growth Fungal multicellularity -1.878122
XANPAGTX0501_004244-T1 IPR012337 IPR Ribonuclease H-like superfamily Cell division, proliferation and growth Fungal multicellularity -1.139706
XANPAGTX0501_004628-T1 IPR012337 IPR Ribonuclease H-like superfamily Cell division, proliferation and growth Fungal multicellularity -1.792127
XANPAGTX0501_003124-T1 IPR001461 IPR Aspartic peptidase A1 family Cell surface and cell wall proteins Fungal multicellularity -1.348872
XANPAGTX0501_005735-T1 IPR018824 IPR Conidiation-specific protein 6 Cell surface and cell wall proteins Fungal multicellularity -2.102015
XANPAGTX0501_006327-T1 IPR018466 IPR Yeast cell wall synthesis Kre9/Knh1-like, N-terminal Cell wall biosynthesis Fungal multicellularity -2.649849
XANPAGTX0501_000203-T1 IPR037176 IPR Osmotin/thaumatin-like superfamily Cell wall remodeling Fungal multicellularity -1.040557
XANPAGTX0501_001856-T1 IPR037176 IPR Osmotin/thaumatin-like superfamily Cell wall remodeling Fungal multicellularity -2.592477
XANPAGTX0501_007833-T1 IPR002889 IPR Carbohydrate-binding WSC Cell wall remodeling Fungal multicellularity -1.343993
XANPAGTX0501_009511-T1 GH16 CAZy act on beta-1,4 or beta-1,3 glycosidic bonds in glucans and galactans Cell wall remodeling Fungal multicellularity -1.533303
XANPAGTX0501_006767-T1 IPR017956 IPR AT hook, DNA-binding motif Chromatin regulation Expression regulation -1.001121
XANPAGTX0501_001064-T1 IPR021765 IPR Mycotoxin biosynthesis protein UstYa-like Defense Fungal multicellularity -1.621988
XANPAGTX0501_001643-T1 IPR001810 IPR F-box domain Protein ubiquitination Fungal multicellularity -1.910689
XANPAGTX0501_003212-T1 IPR001810 IPR F-box domain Protein ubiquitination Fungal multicellularity -1.757104
XANPAGTX0501_003213-T1 IPR001810 IPR F-box domain Protein ubiquitination Fungal multicellularity -1.804291
XANPAGTX0501_003264-T1 IPR000210 IPR BTB/POZ domain Protein ubiquitination Fungal multicellularity -1.264968
XANPAGTX0501_005550-T1 IPR001810 IPR F-box domain Protein ubiquitination Fungal multicellularity -1.294683
XANPAGTX0501_005620-T1 IPR017907 IPR Zinc finger; RING-type; conserved site Protein ubiquitination Fungal multicellularity -1.973360
XANPAGTX0501_006203-T1 IPR017907 IPR Zinc finger; RING-type; conserved site Protein ubiquitination Fungal multicellularity -1.386200
XANPAGTX0501_007869-T1 IPR000210 IPR BTB/POZ domain Protein ubiquitination Fungal multicellularity -1.472330
XANPAGTX0501_008856-T1 IPR001810 IPR F-box domain Protein ubiquitination Fungal multicellularity -2.160218
XANPAGTX0501_009316-T1 IPR001810 IPR F-box domain Protein ubiquitination Fungal multicellularity -1.697722
XANPAGTX0501_009738-T1 IPR001810 IPR F-box domain Protein ubiquitination Fungal multicellularity -1.170585
XANPAGTX0501_009942-T1 IPR001810 IPR F-box domain Protein ubiquitination Fungal multicellularity -1.494661
XANPAGTX0501_010380-T1 IPR000210 IPR BTB/POZ domain Protein ubiquitination Fungal multicellularity -1.404538
XANPAGTX0501_001648-T1 IPR000504 IPR RNA recognition motif domain RNA binding proteins Expression regulation -1.214948
XANPAGTX0501_002098-T1 IPR000504 IPR RNA recognition motif domain RNA binding proteins Expression regulation -1.334348
XANPAGTX0501_002123-T1 IPR000504 IPR RNA recognition motif domain RNA binding proteins Expression regulation -1.312729
XANPAGTX0501_004217-T1 IPR000504 IPR RNA recognition motif domain RNA binding proteins Expression regulation -1.766312
XANPAGTX0501_005177-T1 IPR001313 IPR Pumilio RNA-binding repeat RNA binding proteins Expression regulation -1.185673
XANPAGTX0501_002123-T1 IPR007855 IPR RNA-dependent RNA polymerase, eukaryotic-type RNA interference Expression regulation -1.312729
XANPAGTX0501_003775-T1 IPR032474 IPR Protein argonaute, N-terminal RNA interference Expression regulation -1.770114
XANPAGTX0501_003775-T2 IPR032474 IPR Protein argonaute, N-terminal RNA interference Expression regulation -1.260916
XANPAGTX0501_004244-T1 IPR032474 IPR Protein argonaute, N-terminal RNA interference Expression regulation -1.139706
XANPAGTX0501_000420-T1 IPR013087 IPR Zinc finger C2H2-type Transcription factors Expression regulation -1.518444
XANPAGTX0501_001955-T1 IPR036864 IPR Zn(2)-C6 fungal-type DNA-binding domain superfamily Transcription factors Expression regulation -1.387192
XANPAGTX0501_001958-T1 IPR001356 IPR Homeobox domain Transcription factors Expression regulation -1.998637
XANPAGTX0501_005620-T1 IPR013083 IPR Zinc finger, RING/FYVE/PHD-type Transcription factors Expression regulation -1.973360
XANPAGTX0501_005640-T1 IPR013087 IPR Zinc finger C2H2-type Transcription factors Expression regulation -1.380432
XANPAGTX0501_006203-T1 IPR013083 IPR Zinc finger, RING/FYVE/PHD-type Transcription factors Expression regulation -1.386200
XANPAGTX0501_006931-T1 IPR013087 IPR Zinc finger C2H2-type Transcription factors Expression regulation -1.072494
XANPAGTX0501_008005-T1 IPR013083 IPR Zinc finger, RING/FYVE/PHD-type Transcription factors Expression regulation -1.251448
XANPAGTX0501_000281-T1 IPR036259 IPR MFS transporter superfamily Transporters Fungal multicellularity -1.282182
XANPAGTX0501_001825-T1 IPR036259 IPR MFS transporter superfamily Transporters Fungal multicellularity -1.402807
XANPAGTX0501_008594-T1 IPR036259 IPR MFS transporter superfamily Transporters Fungal multicellularity -1.040188
XANPAGTX0501_009737-T1 IPR036259 IPR MFS transporter superfamily Transporters Fungal multicellularity -1.540774
  • Notably, many TFs and ubiquitin degradation proteins

  • Also many transporters, which wasn’t the case in other lists here

  • Enrichment analysis

enrich2<-clusterProfiler::enricher(ap_ea_genes$target_id,
    pAdjustMethod = "none",
    minGSSize = 1,
    maxGSSize = 2000,
    qvalueCutoff = 1,
    universe=ips_data$universe,
    TERM2GENE=ips_data$term2protein,
    TERM2NAME=ips_data$term2name)

enrich_pairwise2<-enrichplot::pairwise_termsim(enrich2)
enrichplot::emapplot(enrich_pairwise2)

Upregulated in edge

  • Bootstrap of the two genes most overexpressed in the edge
plot_bootstrap(ea_so, 
               target_id = ea_sig$target_id[which.max(ea_sig$b)], 
               units = "est_counts", 
               color_by = "part")
plot_bootstrap(ea_so, 
               target_id = ea_sig$target_id[which.max(ea_sig$b[-which.max(ea_sig$b)])], 
               units = "est_counts", 
               color_by = "part")

  • Of the 13 upregulated in edge, 3 have no functional annotations
  • 6 are secreted
ed_ea_genes<-ea_sig %>% filter(change=="edge") %>%
  left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
  select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
ed_ea_genes %>% 
  kable(format = "html", col.names = colnames(ap_ea_genes)) %>%
  kable_styling() %>%
  kableExtra::scroll_box(width = "100%", height = "600px")
target_id b InterPro_new CAZyme_new Protease_new KO secreted_consensus lichen_ortho
XANPAGTX0501_010431-T1 1.523359 NA NA NA FALSE FALSE
XANPAGTX0501_001015-T1 1.339807 IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily NA NA TRUE FALSE
XANPAGTX0501_006189-T1 1.275509 IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily NA NA FALSE FALSE
XANPAGTX0501_002706-T1 1.129817 IPR002129 Pyridoxal phosphate-dependent decarboxylase, IPR015421 Pyridoxal phosphate-dependent transferase, major domain, IPR015424 Pyridoxal phosphate-dependent transferase NA NA FALSE FALSE
XANPAGTX0501_004034-T1 1.121819 NA NA NA TRUE FALSE
XANPAGTX0501_010624-T1 1.121535 IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily NA NA TRUE FALSE
XANPAGTX0501_004943-T2 1.117316 IPR002020 Citrate synthase, IPR016142 Citrate synthase-like, large alpha subdomain, IPR016143 Citrate synthase-like, small alpha subdomain, IPR019810 Citrate synthase active site, IPR036969 Citrate synthase superfamily NA NA K01647 FALSE FALSE
XANPAGTX0501_006869-T1 1.099929 IPR008979 Galactose-binding-like domain superfamily, IPR017853 Glycoside hydrolase superfamily, IPR024655 Asl1-like, glycosyl hydrolase catalytic domain GH128 NA TRUE FALSE
XANPAGTX0501_004633-T1 1.094695 NA NA NA FALSE FALSE
XANPAGTX0501_010430-T1 1.093667 IPR000542 Acyltransferase ChoActase/COT/CPT, IPR001227 Acyl transferase domain superfamily, IPR006162 Phosphopantetheine attachment site, IPR009081 Phosphopantetheine binding ACP domain, IPR011032 GroES-like superfamily, IPR013217 Methyltransferase type 12, IPR013968 Polyketide synthase, ketoreductase domain, IPR014030 Beta-ketoacyl synthase, N-terminal, IPR014031 Beta-ketoacyl synthase, C-terminal, IPR014043 Acyl transferase, IPR016035 Acyl transferase/acyl hydrolase/lysophospholipase, IPR016036 Malonyl-CoA ACP transacylase, ACP-binding, IPR016039 Thiolase-like, IPR020801 None, IPR020806 Polyketide synthase, phosphopantetheine-binding domain, IPR020807 Polyketide synthase, dehydratase domain, IPR020841 Polyketide synthase, beta-ketoacyl synthase domain, IPR020843 Polyketide synthase, enoylreductase domain, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR032821 Polyketide synthase, C-terminal extension, IPR036291 NAD(P)-binding domain superfamily, IPR036736 ACP-like superfamily, IPR039551 Choline/carnitine acyltransferase domain, IPR042104 Polyketide synthase, dehydratase domain superfamily, IPR042231 Choline/Carnitine o-acyltransferase, domain 2, IPR042232 None NA NA K12443 FALSE TRUE
XANPAGTX0501_001458-T1 1.026449 IPR002889 Carbohydrate-binding WSC, IPR018535 Domain of unknown function DUF1996 NA NA TRUE FALSE
XANPAGTX0501_009181-T1 1.024662 IPR008427 Extracellular membrane protein, CFEM domain NA NA TRUE TRUE
XANPAGTX0501_008853-T1 1.003145 IPR009799 EthD domain, IPR011008 Dimeric alpha-beta barrel NA NA FALSE FALSE

Parietin cluster is upregulated in the edge

  • One of the proteins in the parietin BGC, an extra one
plot_bootstrap(ea_so, 
               target_id = "XANPAGTX0501_008853-T1", 
               units = "est_counts", 
               color_by = "part")

  • The main PKS gene is just below the threshold (b = 0.92)
plot_bootstrap(ea_so, 
               target_id = "XANPAGTX0501_008852-T1", 
               units = "est_counts", 
               color_by = "part")

4.2. Power analysis: simple

  • Do we have enough samples for this comparison?
  • Looked at the distribution of corrected p-values (a.k.a. q-values). The graph looks good: close to uniform, with an increase close to 0. If our test was underpowered, we would see an increase of p-vlaues along 0->1, but this is not the case
ggplot(ea_table)+geom_histogram(aes(x=qval))
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 690798 rows containing non-finite values (`stat_bin()`).

  • QQ-plot looks fine
library(MKpower)
qqunif(ea_table$qval, color.line = "orange")

5. How similar are gene lists between comparisons?

Upregulated in the edge

  • Only one gene upregulated compared to the center, and it is also in the second list
library(ggVennDiagram)
## 
## Attaching package: 'ggVennDiagram'
## The following object is masked from 'package:tidyr':
## 
##     unite
venn_e<-list(compared_to_apothecia = ea_sig$target_id[ea_sig$change=="edge"],
               compared_to_center = ec_sig$target_id[ec_sig$b>0.9])
e<-ggVennDiagram(venn_e,label_size = 5,set_size=5)+labs(title = "Upregulated in edge")+theme(title=element_text(size=12))+scale_x_continuous(expand = expansion(mult = .4))
e

Upregulated in the center

  • Compared to apothecia one is upregulated, and it’s not in the second list
venn_c<-list(compared_to_apothecia = ca_sig$target_id[ca_sig$change=="centre"],
               compared_to_edge = ec_sig$target_id[ec_sig$change=="centre"])

c<-ggVennDiagram(venn_c,label_size = 5,set_size=5)+labs(title = "Upregulated in center")+theme(title=element_text(size=12))+scale_x_continuous(expand = expansion(mult = .4))
c

Upregulated in the apothecia

  • These lists are large, and the smaller is almost entirely overlapping with the bigger one
venn_a<-list(compared_to_center = ca_sig$target_id[ca_sig$change=="apothecium"],
               compared_to_edge = ea_sig$target_id[ea_sig$change=="apothecium"])

a<-ggVennDiagram(venn_a,label_size = 5,set_size=5)+labs(title = "Upregulated in apothecia")+theme(title=element_text(size=12))+scale_x_continuous(expand = expansion(mult = .4))
a

6. Comparing apothecia vs center+edge

kal_dirs2 <-kal_dirs2 %>% mutate(part2 = ifelse(part =="apothecia","apothecia","thallus") )
kal_dirs2$part2 <- as.factor(kal_dirs2$part2)
kal_dirs2$thallus<- as.factor(kal_dirs2$thallus)

rhdf5::h5closeAll()
a_so <- sleuth_prep(kal_dirs2,extra_bootstrap_summary = TRUE,filter_target_id = target_id,transformation_function = function(x) log2(x + 0.1))
## Warning in check_num_cores(num_cores): It appears that you are running Sleuth from within Rstudio.
## Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
## If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
## reading in kallisto results
## dropping unused factor levels
## .................
## normalizing est_counts
## A list of target IDs for filtering was found. Using this for filtering
## 11083 targets passed the filter
## normalizing tpm
## merging in metadata
## summarizing bootstraps
## .................
#model that includes only confounding variables
a_so <- sleuth_fit(a_so, ~thallus, 'reduced') 
## fitting measurement error models
## shrinkage estimation
## 1 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000967-T1
## computing variance of betas
#model that includes only both the confounding variable and the variable of interest
a_so  <- sleuth_fit(a_so, ~ thallus + part2, 'full')
## fitting measurement error models
## shrinkage estimation
## 4 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000967-T1, XANPAGTX0501_001127-T1, XANPAGTX0501_002409-T1, XANPAGTX0501_010086-T1
## computing variance of betas
#compare the models
a_so <- sleuth_lrt(a_so, 'reduced', 'full')
a_so <- sleuth_wt(a_so, 'part2thallus')

a_table <- sleuth_results(a_so, 'part2thallus')
a_sig <- a_table %>% tibble::as_tibble() %>% 
  filter( qval <= 0.05, grepl("GTX0501",target_id) ) %>% 
  arrange(desc(b)) %>% mutate(change = if_else(b > 1, "thallus", ifelse(b< -1, "apothecium", "low_logFC")))

table(a_sig$change)
## 
## apothecium  low_logFC    thallus 
##        250       2746          2
library(RColorBrewer)
color_scheme<-c("apothecia"=brewer.pal(3,"Dark2")[1],
                "thallus_centre"=brewer.pal(3,"Dark2")[2], 
               "thallus_edge" =brewer.pal(3,"Dark2")[3] )

plot_pca(a_so, color_by = 'part', text_labels = TRUE,use_filtered=T)+
  theme_bw()+theme(text=element_text(size=7))+
  scale_color_manual(values=color_scheme)

ggsave('../results/tissue_pca.pdf',width = 4.5, height = 3)

Upregulated in thallus

plot_bootstrap(a_so, 
               target_id = a_sig$target_id[which.max(a_sig$b)], 
               units = "est_counts", 
               color_by = "part2")
plot_bootstrap(a_so, 
               target_id = a_sig$target_id[which.max(a_sig$b[-which.max(a_sig$b)])], 
               units = "est_counts", 
               color_by = "part2")

  • XANPAGTX0501_009376-T1 was not DGE in the edge/apothecia and center/apothecia comparisons
    • is a ribosomal protein
  • XANPAGTX0501_004633-T1 was upregulated in the edge in the edge/apothecia, and nearly upregulated in center/apothecia (b value = 0.977)
    • has no annotations, see above
a_genes<-a_sig %>% filter(b>0.9) %>%
  left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
  select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
a_genes %>% 
  kable(format = "html", col.names = colnames(a_genes)) %>%
  kable_styling() %>%
  kableExtra::scroll_box(width = "100%", height = "600px")
target_id b InterPro_new CAZyme_new Protease_new KO secreted_consensus lichen_ortho
XANPAGTX0501_009376-T1 2.4961545 IPR043141 Ribosomal protein L10-like domain superfamily NA NA K02864 FALSE FALSE
XANPAGTX0501_004633-T1 1.0318823 NA NA NA FALSE FALSE
XANPAGTX0501_009913-T1 0.9922726 NA NA NA FALSE TRUE
XANPAGTX0501_002706-T1 0.9523073 IPR002129 Pyridoxal phosphate-dependent decarboxylase, IPR015421 Pyridoxal phosphate-dependent transferase, major domain, IPR015424 Pyridoxal phosphate-dependent transferase NA NA FALSE FALSE

Upregulated in apothecia

  • Of the 250 upregulated in apothecia, 171 have no functional annotations
  • 24 are secreted
ap_a_genes<-a_sig %>% filter(change=="apothecium") %>%
  left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
  select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
ap_a_genes %>% 
  kable(format = "html", col.names = colnames(ap_a_genes)) %>%
  kable_styling() %>%
  kableExtra::scroll_box(width = "100%", height = "600px")
target_id b InterPro_new CAZyme_new Protease_new KO secreted_consensus lichen_ortho
XANPAGTX0501_007851-T1 -1.000996 NA NA NA FALSE FALSE
XANPAGTX0501_009787-T1 -1.001679 NA NA NA FALSE FALSE
XANPAGTX0501_000938-T1 -1.002687 NA NA NA FALSE FALSE
XANPAGTX0501_007833-T1 -1.003237 IPR002889 Carbohydrate-binding WSC, IPR018535 Domain of unknown function DUF1996 NA NA FALSE FALSE
XANPAGTX0501_001498-T1 -1.006175 IPR012340 Nucleic acid-binding, OB-fold NA NA FALSE FALSE
XANPAGTX0501_005188-T1 -1.006230 NA NA NA FALSE FALSE
XANPAGTX0501_003775-T2 -1.015597 IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily NA NA K11593 FALSE FALSE
XANPAGTX0501_007473-T1 -1.021407 NA NA NA FALSE FALSE
XANPAGTX0501_003790-T1 -1.024429 NA NA NA FALSE TRUE
XANPAGTX0501_006420-T1 -1.025603 NA NA NA FALSE FALSE
XANPAGTX0501_001955-T1 -1.028447 IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain, IPR001451 Hexapeptide repeat, IPR002110 Ankyrin repeat, IPR011004 Trimeric LpxA-like superfamily, IPR018357 Hexapeptide transferase, conserved site, IPR020683 Domain of unknown function DUF3447, IPR024688 Maltose/galactoside acetyltransferase, IPR036770 Ankyrin repeat-containing domain superfamily, IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily NA NA FALSE FALSE
XANPAGTX0501_003033-T1 -1.030286 NA NA NA FALSE FALSE
XANPAGTX0501_002054-T1 -1.034049 NA NA NA FALSE TRUE
XANPAGTX0501_003124-T1 -1.035285 IPR001461 Aspartic peptidase A1 family, IPR001969 Aspartic peptidase, active site, IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain, IPR034164 Pepsin-like domain NA A01A TRUE FALSE
XANPAGTX0501_002946-T1 -1.035401 NA NA NA FALSE TRUE
XANPAGTX0501_002142-T1 -1.036917 NA NA NA FALSE FALSE
XANPAGTX0501_009581-T1 -1.037279 NA NA NA FALSE FALSE
XANPAGTX0501_004753-T1 -1.037567 NA NA NA FALSE FALSE
XANPAGTX0501_003765-T1 -1.038156 IPR000420 Yeast PIR protein repeat NA NA TRUE FALSE
XANPAGTX0501_004978-T1 -1.047426 NA NA NA TRUE FALSE
XANPAGTX0501_004466-T1 -1.048483 IPR000490 Glycoside hydrolase family 17, IPR017853 Glycoside hydrolase superfamily, IPR018620 Ubiquitin 3 binding protein But2, C-terminal NA NA TRUE FALSE
XANPAGTX0501_006422-T1 -1.053965 NA NA NA FALSE FALSE
XANPAGTX0501_005317-T1 -1.054307 NA NA NA TRUE FALSE
XANPAGTX0501_006975-T1 -1.054818 NA NA NA FALSE FALSE
XANPAGTX0501_000622-T1 -1.055181 NA NA NA FALSE FALSE
XANPAGTX0501_002098-T1 -1.056175 IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily NA NA FALSE FALSE
XANPAGTX0501_007365-T1 -1.056362 NA NA NA FALSE FALSE
XANPAGTX0501_004102-T1 -1.058681 IPR000420 Yeast PIR protein repeat NA NA K26550 TRUE FALSE
XANPAGTX0501_001825-T1 -1.063406 IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily NA NA FALSE FALSE
XANPAGTX0501_001223-T1 -1.064214 NA NA NA FALSE FALSE
XANPAGTX0501_005815-T1 -1.064277 IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily NA NA FALSE FALSE
XANPAGTX0501_000036-T1 -1.068838 IPR006640 SprT-like NA NA FALSE FALSE
XANPAGTX0501_002019-T1 -1.070414 NA NA NA FALSE FALSE
XANPAGTX0501_005619-T1 -1.070482 NA NA NA FALSE FALSE
XANPAGTX0501_009599-T1 -1.070929 NA NA NA FALSE FALSE
XANPAGTX0501_001964-T1 -1.071179 IPR001611 Leucine-rich repeat, IPR003591 Leucine-rich repeat, typical subtype, IPR019487 RAM signalling pathway, SOG2, IPR032675 Leucine-rich repeat domain superfamily NA NA FALSE FALSE
XANPAGTX0501_000888-T1 -1.071659 NA NA NA FALSE FALSE
XANPAGTX0501_009795-T2 -1.071736 IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily NA NA FALSE FALSE
XANPAGTX0501_008200-T1 -1.073076 NA NA NA FALSE FALSE
XANPAGTX0501_008888-T1 -1.075701 IPR007527 Zinc finger, SWIM-type NA NA FALSE TRUE
XANPAGTX0501_010001-T1 -1.075953 NA NA NA FALSE FALSE
XANPAGTX0501_010379-T1 -1.076421 NA NA NA FALSE FALSE
XANPAGTX0501_001965-T1 -1.078800 NA NA NA FALSE FALSE
XANPAGTX0501_010094-T1 -1.079269 NA NA NA FALSE FALSE
XANPAGTX0501_006459-T1 -1.089552 NA NA NA FALSE FALSE
XANPAGTX0501_002123-T1 -1.092697 IPR000504 RNA recognition motif domain, IPR007855 RNA-dependent RNA polymerase, eukaryotic-type, IPR035979 RNA-binding domain superfamily NA NA K11699 FALSE FALSE
XANPAGTX0501_009326-T1 -1.097552 NA NA NA FALSE FALSE
XANPAGTX0501_001948-T1 -1.099351 NA NA NA FALSE FALSE
XANPAGTX0501_009293-T1 -1.101651 NA NA NA TRUE FALSE
XANPAGTX0501_007899-T1 -1.103335 NA NA NA FALSE FALSE
XANPAGTX0501_000420-T1 -1.104047 IPR013087 Zinc finger C2H2-type NA NA FALSE FALSE
XANPAGTX0501_006246-T1 -1.104366 NA NA NA FALSE FALSE
XANPAGTX0501_006114-T1 -1.104804 IPR001680 WD40 repeat, IPR015943 WD40/YVTN repeat-like-containing domain superfamily, IPR036322 WD40-repeat-containing domain superfamily NA NA K12782 FALSE FALSE
XANPAGTX0501_006310-T1 -1.105045 IPR022137 Zinc finger protein, DUF3669 domain NA NA FALSE FALSE
XANPAGTX0501_001963-T1 -1.111833 NA NA NA FALSE FALSE
XANPAGTX0501_004008-T1 -1.117183 NA NA NA FALSE FALSE
XANPAGTX0501_002410-T1 -1.117363 NA NA NA FALSE FALSE
XANPAGTX0501_002963-T1 -1.118354 IPR000172 Glucose-methanol-choline oxidoreductase, N-terminal, IPR007867 Glucose-methanol-choline oxidoreductase, C-terminal, IPR012132 Glucose-methanol-choline oxidoreductase, IPR036188 FAD/NAD(P)-binding domain superfamily AA3 NA K00108 TRUE FALSE
XANPAGTX0501_006909-T1 -1.120330 NA NA NA FALSE FALSE
XANPAGTX0501_010145-T1 -1.120565 NA NA NA FALSE TRUE
XANPAGTX0501_005584-T1 -1.124341 NA NA NA FALSE FALSE
XANPAGTX0501_002007-T1 -1.126910 NA NA NA TRUE TRUE
XANPAGTX0501_005278-T1 -1.128439 NA NA NA FALSE FALSE
XANPAGTX0501_000872-T1 -1.128589 NA NA NA FALSE FALSE
XANPAGTX0501_001710-T1 -1.130646 IPR007577 Glycosyltransferase, DXD sugar-binding motif, IPR029044 Nucleotide-diphospho-sugar transferases GT32 NA FALSE FALSE
XANPAGTX0501_007869-T1 -1.136332 IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily NA NA FALSE FALSE
XANPAGTX0501_009511-T1 -1.136478 IPR000757 Glycoside hydrolase family 16, IPR001002 Chitin-binding, type 1, IPR008264 Beta-glucanase, IPR013320 Concanavalin A-like lectin/glucanase domain superfamily, IPR036861 Endochitinase-like superfamily GH16 NA K01216 TRUE FALSE
XANPAGTX0501_000691-T1 -1.140810 NA NA NA FALSE TRUE
XANPAGTX0501_010007-T1 -1.146366 NA NA NA FALSE FALSE
XANPAGTX0501_001820-T2 -1.147375 IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain NA NA FALSE FALSE
XANPAGTX0501_008863-T1 -1.149308 NA NA NA FALSE FALSE
XANPAGTX0501_010381-T1 -1.157248 IPR002293 Amino acid/polyamine transporter I NA NA K03294 FALSE FALSE
XANPAGTX0501_003361-T1 -1.157393 NA NA NA TRUE FALSE
XANPAGTX0501_009666-T1 -1.163354 NA NA NA FALSE FALSE
XANPAGTX0501_000910-T1 -1.164861 NA NA NA FALSE FALSE
XANPAGTX0501_009942-T1 -1.164912 IPR001810 F-box domain, IPR036047 F-box-like domain superfamily NA NA FALSE FALSE
XANPAGTX0501_008874-T1 -1.168644 NA NA NA FALSE TRUE
XANPAGTX0501_005296-T1 -1.170842 IPR018750 Protein of unknown function DUF2306, membrane NA NA FALSE FALSE
XANPAGTX0501_004853-T1 -1.170891 IPR000719 Protein kinase domain, IPR000961 AGC-kinase, C-terminal, IPR011009 Protein kinase-like domain superfamily NA NA FALSE FALSE
XANPAGTX0501_001512-T1 -1.171326 NA NA NA FALSE FALSE
XANPAGTX0501_006203-T1 -1.175049 IPR001841 Zinc finger, RING-type, IPR002867 IBR domain, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site NA NA FALSE FALSE
XANPAGTX0501_001436-T1 -1.178216 IPR002048 EF-hand domain, IPR011992 EF-hand domain pair, IPR018247 EF-Hand 1, calcium-binding site NA NA FALSE FALSE
XANPAGTX0501_007750-T1 -1.181450 IPR027417 P-loop containing nucleoside triphosphate hydrolase NA NA FALSE FALSE
XANPAGTX0501_002820-T1 -1.183558 NA NA NA FALSE TRUE
XANPAGTX0501_010051-T1 -1.184568 NA NA NA FALSE FALSE
XANPAGTX0501_003247-T1 -1.184643 IPR001878 Zinc finger, CCHC-type, IPR025836 Zinc knuckle CX2CX4HX4C, IPR036875 Zinc finger, CCHC-type superfamily NA NA K09250 FALSE FALSE
XANPAGTX0501_009621-T1 -1.188204 NA NA NA FALSE FALSE
XANPAGTX0501_005620-T1 -1.188513 IPR001841 Zinc finger, RING-type, IPR004331 SPX domain, IPR011016 Zinc finger, RING-CH-type, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site NA NA FALSE TRUE
XANPAGTX0501_009321-T1 -1.190228 NA NA NA FALSE FALSE
XANPAGTX0501_003448-T1 -1.191987 NA NA NA TRUE TRUE
XANPAGTX0501_009141-T1 -1.192722 NA NA NA FALSE FALSE
XANPAGTX0501_009887-T1 -1.200786 NA NA NA TRUE FALSE
XANPAGTX0501_000610-T1 -1.207426 NA NA NA FALSE FALSE
XANPAGTX0501_001643-T1 -1.215746 IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily NA NA FALSE TRUE
XANPAGTX0501_010380-T1 -1.223224 IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily NA NA FALSE TRUE
XANPAGTX0501_007403-T1 -1.228285 NA NA NA FALSE TRUE
XANPAGTX0501_001082-T1 -1.232060 IPR004853 Sugar phosphate transporter domain NA NA K26222 FALSE FALSE
XANPAGTX0501_004416-T1 -1.234261 IPR000246 Peptidase T2, asparaginase 2, IPR029055 Nucleophile aminohydrolases, N-terminal, IPR037464 Threonine aspartase 1 NA T02 K08657 FALSE FALSE
XANPAGTX0501_001064-T1 -1.234644 IPR021765 Mycotoxin biosynthesis protein UstYa-like NA NA FALSE FALSE
XANPAGTX0501_001061-T1 -1.235309 IPR002328 Alcohol dehydrogenase, zinc-type, conserved site, IPR011032 GroES-like superfamily, IPR013149 Alcohol dehydrogenase-like, C-terminal, IPR013154 Alcohol dehydrogenase-like, N-terminal, IPR020843 Polyketide synthase, enoylreductase domain, IPR036291 NAD(P)-binding domain superfamily NA NA FALSE FALSE
XANPAGTX0501_004018-T2 -1.235695 IPR011009 Protein kinase-like domain superfamily, IPR016477 Fructosamine/Ketosamine-3-kinase NA NA FALSE TRUE
XANPAGTX0501_007231-T1 -1.240318 NA NA NA FALSE FALSE
XANPAGTX0501_009316-T1 -1.246011 IPR001810 F-box domain, IPR036047 F-box-like domain superfamily NA NA FALSE FALSE
XANPAGTX0501_003283-T1 -1.246856 NA NA NA FALSE FALSE
XANPAGTX0501_007244-T1 -1.249898 NA NA NA FALSE FALSE
XANPAGTX0501_008533-T1 -1.253515 NA NA NA FALSE FALSE
XANPAGTX0501_007343-T1 -1.255419 NA NA NA FALSE FALSE
XANPAGTX0501_001952-T1 -1.257146 NA NA NA FALSE FALSE
XANPAGTX0501_001950-T1 -1.259001 NA NA NA FALSE FALSE
XANPAGTX0501_002213-T1 -1.262177 IPR000629 ATP-dependent RNA helicase DEAD-box, conserved site, IPR001650 Helicase, C-terminal, IPR011545 DEAD/DEAH box helicase domain, IPR014001 Helicase superfamily 1/2, ATP-binding domain, IPR014014 RNA helicase, DEAD-box type, Q motif, IPR027417 P-loop containing nucleoside triphosphate hydrolase NA NA FALSE FALSE
XANPAGTX0501_001951-T1 -1.262779 NA NA NA FALSE FALSE
XANPAGTX0501_000604-T1 -1.264223 NA NA NA FALSE FALSE
XANPAGTX0501_010117-T1 -1.267941 IPR002110 Ankyrin repeat, IPR011009 Protein kinase-like domain superfamily, IPR016477 Fructosamine/Ketosamine-3-kinase, IPR020683 Domain of unknown function DUF3447, IPR036770 Ankyrin repeat-containing domain superfamily NA NA K15523 FALSE FALSE
XANPAGTX0501_000697-T1 -1.273117 NA NA NA TRUE FALSE
XANPAGTX0501_008628-T1 -1.274944 IPR023346 Lysozyme-like domain superfamily NA NA FALSE TRUE
XANPAGTX0501_001956-T1 -1.276631 NA NA NA FALSE FALSE
XANPAGTX0501_000398-T1 -1.277824 NA NA NA FALSE FALSE
XANPAGTX0501_002057-T1 -1.282644 NA NA NA FALSE FALSE
XANPAGTX0501_001888-T1 -1.289043 NA NA NA FALSE FALSE
XANPAGTX0501_006449-T1 -1.291222 NA NA NA FALSE FALSE
XANPAGTX0501_008008-T1 -1.291576 NA NA NA FALSE FALSE
XANPAGTX0501_003282-T1 -1.293552 NA NA NA FALSE FALSE
XANPAGTX0501_008426-T1 -1.294283 NA NA NA FALSE FALSE
XANPAGTX0501_005613-T1 -1.294861 IPR003615 HNH nuclease NA NA FALSE TRUE
XANPAGTX0501_007464-T1 -1.298109 NA NA NA FALSE FALSE
XANPAGTX0501_007870-T1 -1.300798 NA NA NA FALSE FALSE
XANPAGTX0501_006245-T1 -1.301264 NA NA NA TRUE TRUE
XANPAGTX0501_008420-T1 -1.301707 NA NA NA FALSE FALSE
XANPAGTX0501_001947-T1 -1.303157 NA NA NA FALSE FALSE
XANPAGTX0501_006330-T1 -1.307915 NA NA NA FALSE FALSE
XANPAGTX0501_000892-T1 -1.309666 NA NA NA FALSE FALSE
XANPAGTX0501_010304-T1 -1.314210 NA NA NA FALSE FALSE
XANPAGTX0501_001362-T1 -1.314577 NA NA NA FALSE FALSE
XANPAGTX0501_004628-T1 -1.317480 IPR002156 Ribonuclease H domain, IPR012337 Ribonuclease H-like superfamily, IPR036397 Ribonuclease H superfamily NA NA K03469 FALSE FALSE
XANPAGTX0501_001330-T1 -1.320530 NA NA NA FALSE TRUE
XANPAGTX0501_005658-T1 -1.322458 IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily NA NA FALSE FALSE
XANPAGTX0501_005402-T1 -1.324043 NA NA NA FALSE TRUE
XANPAGTX0501_002165-T1 -1.325802 NA NA NA FALSE FALSE
XANPAGTX0501_008534-T1 -1.327391 NA NA NA FALSE FALSE
XANPAGTX0501_002170-T1 -1.328820 NA NA NA FALSE FALSE
XANPAGTX0501_009317-T1 -1.330469 IPR008979 Galactose-binding-like domain superfamily NA NA TRUE FALSE
XANPAGTX0501_005394-T1 -1.334492 IPR002575 Aminoglycoside phosphotransferase, IPR011009 Protein kinase-like domain superfamily NA NA FALSE FALSE
XANPAGTX0501_005631-T1 -1.336475 IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily NA NA FALSE FALSE
XANPAGTX0501_002103-T1 -1.336659 IPR036910 High mobility group box domain superfamily NA NA FALSE FALSE
XANPAGTX0501_008856-T1 -1.339511 IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily NA NA FALSE TRUE
XANPAGTX0501_000681-T1 -1.344215 NA NA NA FALSE FALSE
XANPAGTX0501_002185-T1 -1.352061 NA NA NA FALSE FALSE
XANPAGTX0501_003775-T1 -1.352148 IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily NA NA K11593 FALSE FALSE
XANPAGTX0501_004580-T1 -1.355977 IPR007292 Nuclear fusion protein Kar5 NA NA FALSE FALSE
XANPAGTX0501_001010-T1 -1.356734 NA NA NA FALSE FALSE
XANPAGTX0501_002104-T1 -1.360844 NA NA NA FALSE FALSE
XANPAGTX0501_004494-T1 -1.362189 NA NA NA FALSE FALSE
XANPAGTX0501_001859-T1 -1.367755 NA NA NA FALSE TRUE
XANPAGTX0501_000025-T1 -1.368135 NA NA NA FALSE TRUE
XANPAGTX0501_005597-T1 -1.371604 IPR006421 Glycogen debranching enzyme, metazoa, IPR008928 Six-hairpin glycosidase superfamily, IPR012341 Six-hairpin glycosidase-like superfamily, IPR017853 Glycoside hydrolase superfamily, IPR029436 Eukaryotic glycogen debranching enzyme, N-terminal domain, IPR032788 Glycogen debranching enzyme, central domain, IPR032790 Glycogen debranching enzyme, C-terminal, IPR032792 Glycogen debranching enzyme, glucanotransferase domain GH133 NA K01196 FALSE FALSE
XANPAGTX0501_004950-T1 -1.372326 NA NA NA FALSE FALSE
XANPAGTX0501_005048-T1 -1.374486 NA NA NA FALSE FALSE
XANPAGTX0501_004217-T1 -1.376777 IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily NA NA K24990 FALSE FALSE
XANPAGTX0501_000005-T1 -1.378844 NA NA NA FALSE FALSE
XANPAGTX0501_003212-T1 -1.384927 IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily NA NA FALSE TRUE
XANPAGTX0501_002763-T1 -1.389644 NA NA NA FALSE FALSE
XANPAGTX0501_002163-T1 -1.392989 NA NA NA FALSE FALSE
XANPAGTX0501_003213-T1 -1.399730 IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily NA NA FALSE TRUE
XANPAGTX0501_004493-T1 -1.400770 NA NA NA FALSE FALSE
XANPAGTX0501_002166-T1 -1.400943 NA NA NA FALSE FALSE
XANPAGTX0501_010280-T1 -1.404057 NA NA NA FALSE FALSE
XANPAGTX0501_006016-T1 -1.404604 IPR008928 Six-hairpin glycosidase superfamily, IPR031335 Glycosyl hydrolase family 63, C-terminal GH63 NA FALSE FALSE
XANPAGTX0501_001333-T1 -1.411305 NA NA NA FALSE TRUE
XANPAGTX0501_004104-T1 -1.419256 IPR001214 SET domain, IPR011990 Tetratricopeptide-like helical domain superfamily NA NA FALSE FALSE
XANPAGTX0501_007067-T1 -1.420720 NA NA NA FALSE TRUE
XANPAGTX0501_007300-T1 -1.423032 NA NA NA FALSE FALSE
XANPAGTX0501_004414-T1 -1.423458 IPR027417 P-loop containing nucleoside triphosphate hydrolase NA NA FALSE TRUE
XANPAGTX0501_001605-T1 -1.425833 NA NA NA FALSE FALSE
XANPAGTX0501_006255-T1 -1.434751 NA NA NA FALSE FALSE
XANPAGTX0501_000647-T1 -1.440550 IPR000571 Zinc finger, CCCH-type NA NA FALSE FALSE
XANPAGTX0501_005615-T1 -1.440903 NA NA NA FALSE FALSE
XANPAGTX0501_006974-T1 -1.441975 NA NA NA FALSE FALSE
XANPAGTX0501_006957-T1 -1.443602 NA NA NA FALSE FALSE
XANPAGTX0501_006910-T1 -1.458293 NA NA NA FALSE FALSE
XANPAGTX0501_001612-T1 -1.458506 NA NA NA FALSE FALSE
XANPAGTX0501_007871-T1 -1.463016 NA NA NA FALSE TRUE
XANPAGTX0501_009582-T1 -1.469666 NA NA NA FALSE FALSE
XANPAGTX0501_009615-T1 -1.478640 IPR035940 CAP superfamily NA NA TRUE FALSE
XANPAGTX0501_001953-T1 -1.483265 NA NA NA FALSE FALSE
XANPAGTX0501_009139-T1 -1.494375 IPR001876 Zinc finger, RanBP2-type NA NA FALSE FALSE
XANPAGTX0501_005630-T1 -1.497428 IPR036928 Amidase signature (AS) superfamily NA NA FALSE FALSE
XANPAGTX0501_004891-T1 -1.501545 NA NA NA FALSE FALSE
XANPAGTX0501_002522-T1 -1.504550 NA NA NA FALSE FALSE
XANPAGTX0501_005612-T1 -1.506602 NA NA NA FALSE TRUE
XANPAGTX0501_000893-T1 -1.508341 NA NA NA FALSE FALSE
XANPAGTX0501_005061-T1 -1.508665 NA NA NA TRUE FALSE
XANPAGTX0501_007873-T1 -1.510868 NA NA NA FALSE TRUE
XANPAGTX0501_001958-T1 -1.511188 IPR001356 Homeobox domain, IPR009057 Homeobox-like domain superfamily, IPR017970 Homeobox, conserved site NA NA FALSE FALSE
XANPAGTX0501_000194-T1 -1.511338 IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR013780 Glycosyl hydrolase, all-beta, IPR017853 Glycoside hydrolase superfamily GH13 NA K01176 FALSE FALSE
XANPAGTX0501_003572-T1 -1.519271 IPR001087 GDSL lipase/esterase, IPR036514 SGNH hydrolase superfamily CE16 NA TRUE FALSE
XANPAGTX0501_002183-T1 -1.522262 NA NA NA FALSE FALSE
XANPAGTX0501_005279-T1 -1.523896 NA NA NA FALSE FALSE
XANPAGTX0501_008041-T1 -1.527220 NA NA NA TRUE FALSE
XANPAGTX0501_005614-T1 -1.527719 NA NA NA FALSE FALSE
XANPAGTX0501_001538-T1 -1.528884 NA NA NA FALSE FALSE
XANPAGTX0501_001954-T1 -1.534783 NA NA NA FALSE FALSE
XANPAGTX0501_001414-T1 -1.537299 NA NA NA FALSE FALSE
XANPAGTX0501_001910-T1 -1.539771 NA NA NA FALSE FALSE
XANPAGTX0501_010303-T1 -1.542026 NA NA NA FALSE FALSE
XANPAGTX0501_004520-T1 -1.559567 NA NA NA FALSE FALSE
XANPAGTX0501_007262-T1 -1.569541 NA NA NA FALSE TRUE
XANPAGTX0501_010203-T1 -1.569541 NA NA NA FALSE TRUE
XANPAGTX0501_008090-T1 -1.570035 NA NA NA FALSE FALSE
XANPAGTX0501_009318-T1 -1.577677 IPR011333 SKP1/BTB/POZ domain superfamily NA NA FALSE FALSE
XANPAGTX0501_002164-T1 -1.582652 NA NA NA FALSE FALSE
XANPAGTX0501_002184-T1 -1.584723 NA NA NA FALSE FALSE
XANPAGTX0501_005735-T1 -1.620055 IPR018824 Conidiation-specific protein 6 NA NA FALSE FALSE
XANPAGTX0501_004521-T1 -1.625040 IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily NA NA FALSE FALSE
XANPAGTX0501_002172-T1 -1.626040 NA NA NA FALSE FALSE
XANPAGTX0501_001967-T1 -1.629031 NA NA NA FALSE FALSE
XANPAGTX0501_008009-T1 -1.631945 NA NA NA FALSE FALSE
XANPAGTX0501_009605-T1 -1.639551 NA NA NA FALSE FALSE
XANPAGTX0501_009619-T1 -1.640066 NA NA NA FALSE FALSE
XANPAGTX0501_001611-T1 -1.646921 NA NA NA FALSE FALSE
XANPAGTX0501_005766-T1 -1.650350 NA NA NA FALSE FALSE
XANPAGTX0501_002182-T1 -1.670548 NA NA NA FALSE FALSE
XANPAGTX0501_008782-T1 -1.681484 NA NA NA FALSE FALSE
XANPAGTX0501_009786-T1 -1.691780 NA NA NA FALSE FALSE
XANPAGTX0501_001962-T1 -1.692967 NA NA NA FALSE FALSE
XANPAGTX0501_007872-T1 -1.694556 NA NA NA FALSE TRUE
XANPAGTX0501_006253-T1 -1.695976 IPR014849 EKC/KEOPS complex, subunit Gon7 NA NA FALSE FALSE
XANPAGTX0501_008331-T1 -1.707064 NA NA NA FALSE FALSE
XANPAGTX0501_003209-T1 -1.709229 NA NA NA FALSE FALSE
XANPAGTX0501_000193-T1 -1.729825 IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR017853 Glycoside hydrolase superfamily GH13 NA FALSE FALSE
XANPAGTX0501_001960-T1 -1.733269 NA NA NA FALSE FALSE
XANPAGTX0501_006951-T1 -1.742660 NA NA NA FALSE FALSE
XANPAGTX0501_008007-T1 -1.745209 NA NA NA FALSE FALSE
XANPAGTX0501_010596-T1 -1.748698 NA NA NA FALSE FALSE
XANPAGTX0501_005814-T1 -1.760286 NA NA NA FALSE FALSE
XANPAGTX0501_008284-T1 -1.771059 IPR029044 Nucleotide-diphospho-sugar transferases GT2_Glyco_tranf_2 NA FALSE FALSE
XANPAGTX0501_009926-T1 -1.775143 NA NA NA FALSE FALSE
XANPAGTX0501_009602-T1 -1.777131 NA NA NA FALSE FALSE
XANPAGTX0501_001063-T1 -1.783787 NA NA NA TRUE FALSE
XANPAGTX0501_007397-T1 -1.849425 NA NA NA FALSE FALSE
XANPAGTX0501_007900-T1 -1.867603 NA NA NA FALSE TRUE
XANPAGTX0501_000378-T1 -1.880561 NA NA NA FALSE FALSE
XANPAGTX0501_004966-T1 -1.889077 NA NA NA FALSE FALSE
XANPAGTX0501_001856-T1 -1.894636 IPR037176 Osmotin/thaumatin-like superfamily NA NA TRUE TRUE
XANPAGTX0501_006327-T1 -1.922253 IPR018466 Yeast cell wall synthesis Kre9/Knh1-like, N-terminal NA NA TRUE FALSE
XANPAGTX0501_002506-T1 -1.931043 NA NA NA FALSE FALSE
XANPAGTX0501_003211-T1 -2.074356 NA NA NA FALSE FALSE
XANPAGTX0501_008109-T1 -2.159140 IPR004143 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain NA NA K03800 FALSE FALSE
XANPAGTX0501_004085-T1 -2.298435 IPR000420 Yeast PIR protein repeat NA NA K26550 TRUE FALSE
XANPAGTX0501_008519-T2 -2.955922 NA NA NA FALSE FALSE
XANPAGTX0501_001156-T3 -3.105399 IPR003822 Paired amphipathic helix, IPR013194 Histone deacetylase interacting domain, IPR031693 Sin3, C-terminal, IPR036600 Paired amphipathic helix superfamily NA NA K11644 FALSE FALSE
  • Selected only genes that are potentially multicellularity related
mult_gene_table_ap3<-mult_gene_table %>% inner_join(a_sig %>% filter(change=="apothecium") %>% select(target_id,b),by=c("TranscriptID"="target_id")) %>% arrange(Function)

mult_gene_table_ap3 %>% 
  kable(format = "html", col.names = colnames(mult_gene_table_ap3)) %>%
  kable_styling() %>%
  kableExtra::scroll_box(width = "100%", height = "600px")
TranscriptID ID Annotation_type Description Function Function_type b
XANPAGTX0501_001061-T1 IPR013149 IPR Alcohol dehydrogenase-like, C-terminal Acetyl-CoA production and metabolism Fungal multicellularity -1.235309
XANPAGTX0501_005597-T1 IPR032788 IPR Glycogen debranching enzyme, central domain Carbohydrate storage Fungal multicellularity -1.371604
XANPAGTX0501_000647-T1 IPR000571 IPR Zinc finger, CCCH-type Cell division, proliferation and growth Fungal multicellularity -1.440550
XANPAGTX0501_002213-T1 IPR001650 IPR Helicase, C-terminal Cell division, proliferation and growth Fungal multicellularity -1.262177
XANPAGTX0501_003775-T1 IPR012337 IPR Ribonuclease H-like superfamily Cell division, proliferation and growth Fungal multicellularity -1.352148
XANPAGTX0501_003775-T2 IPR012337 IPR Ribonuclease H-like superfamily Cell division, proliferation and growth Fungal multicellularity -1.015597
XANPAGTX0501_004104-T1 IPR001214 IPR SET domain Cell division, proliferation and growth Fungal multicellularity -1.419256
XANPAGTX0501_004628-T1 IPR012337 IPR Ribonuclease H-like superfamily Cell division, proliferation and growth Fungal multicellularity -1.317480
XANPAGTX0501_003124-T1 IPR001461 IPR Aspartic peptidase A1 family Cell surface and cell wall proteins Fungal multicellularity -1.035285
XANPAGTX0501_005735-T1 IPR018824 IPR Conidiation-specific protein 6 Cell surface and cell wall proteins Fungal multicellularity -1.620055
XANPAGTX0501_006327-T1 IPR018466 IPR Yeast cell wall synthesis Kre9/Knh1-like, N-terminal Cell wall biosynthesis Fungal multicellularity -1.922253
XANPAGTX0501_001856-T1 IPR037176 IPR Osmotin/thaumatin-like superfamily Cell wall remodeling Fungal multicellularity -1.894636
XANPAGTX0501_007833-T1 IPR002889 IPR Carbohydrate-binding WSC Cell wall remodeling Fungal multicellularity -1.003237
XANPAGTX0501_009511-T1 GH16 CAZy act on beta-1,4 or beta-1,3 glycosidic bonds in glucans and galactans Cell wall remodeling Fungal multicellularity -1.136478
XANPAGTX0501_001064-T1 IPR021765 IPR Mycotoxin biosynthesis protein UstYa-like Defense Fungal multicellularity -1.234644
XANPAGTX0501_001643-T1 IPR001810 IPR F-box domain Protein ubiquitination Fungal multicellularity -1.215746
XANPAGTX0501_003212-T1 IPR001810 IPR F-box domain Protein ubiquitination Fungal multicellularity -1.384927
XANPAGTX0501_003213-T1 IPR001810 IPR F-box domain Protein ubiquitination Fungal multicellularity -1.399730
XANPAGTX0501_005620-T1 IPR017907 IPR Zinc finger; RING-type; conserved site Protein ubiquitination Fungal multicellularity -1.188513
XANPAGTX0501_005815-T1 IPR000210 IPR BTB/POZ domain Protein ubiquitination Fungal multicellularity -1.064277
XANPAGTX0501_006203-T1 IPR017907 IPR Zinc finger; RING-type; conserved site Protein ubiquitination Fungal multicellularity -1.175049
XANPAGTX0501_007869-T1 IPR000210 IPR BTB/POZ domain Protein ubiquitination Fungal multicellularity -1.136332
XANPAGTX0501_008856-T1 IPR001810 IPR F-box domain Protein ubiquitination Fungal multicellularity -1.339511
XANPAGTX0501_009316-T1 IPR001810 IPR F-box domain Protein ubiquitination Fungal multicellularity -1.246011
XANPAGTX0501_009942-T1 IPR001810 IPR F-box domain Protein ubiquitination Fungal multicellularity -1.164912
XANPAGTX0501_010380-T1 IPR000210 IPR BTB/POZ domain Protein ubiquitination Fungal multicellularity -1.223224
XANPAGTX0501_002098-T1 IPR000504 IPR RNA recognition motif domain RNA binding proteins Expression regulation -1.056175
XANPAGTX0501_002123-T1 IPR000504 IPR RNA recognition motif domain RNA binding proteins Expression regulation -1.092697
XANPAGTX0501_004217-T1 IPR000504 IPR RNA recognition motif domain RNA binding proteins Expression regulation -1.376777
XANPAGTX0501_002123-T1 IPR007855 IPR RNA-dependent RNA polymerase, eukaryotic-type RNA interference Expression regulation -1.092697
XANPAGTX0501_003775-T1 IPR032474 IPR Protein argonaute, N-terminal RNA interference Expression regulation -1.352148
XANPAGTX0501_003775-T2 IPR032474 IPR Protein argonaute, N-terminal RNA interference Expression regulation -1.015597
XANPAGTX0501_000420-T1 IPR013087 IPR Zinc finger C2H2-type Transcription factors Expression regulation -1.104047
XANPAGTX0501_001955-T1 IPR036864 IPR Zn(2)-C6 fungal-type DNA-binding domain superfamily Transcription factors Expression regulation -1.028447
XANPAGTX0501_001958-T1 IPR001356 IPR Homeobox domain Transcription factors Expression regulation -1.511188
XANPAGTX0501_005620-T1 IPR013083 IPR Zinc finger, RING/FYVE/PHD-type Transcription factors Expression regulation -1.188513
XANPAGTX0501_006203-T1 IPR013083 IPR Zinc finger, RING/FYVE/PHD-type Transcription factors Expression regulation -1.175049
XANPAGTX0501_001825-T1 IPR036259 IPR MFS transporter superfamily Transporters Fungal multicellularity -1.063406
  • Enrichment analysis
###enrichment analysis
enrich<-clusterProfiler::enricher(ap_a_genes$target_id,
    pAdjustMethod = "none",
    minGSSize = 1,
    maxGSSize = 2000,
    qvalueCutoff = 1,
    universe=ips_data$universe,
    TERM2GENE=ips_data$term2protein,
    TERM2NAME=ips_data$term2name)

enrich_pairwise<-enrichplot::pairwise_termsim(enrich)
enrichplot::emapplot(enrich_pairwise)

  • Save
pdf(file="../results/apothecia_upr.pdf",width=6,height=5)
enrichplot::emapplot(enrich_pairwise,cex_label_category=0.4,cex_line=0.25,
                     shadowtext=F,cex_pie2axis=0.1,repel=T)
dev.off()
## quartz_off_screen 
##                 2
  • This new set includes almost all of the genes from the center/apothecia comparison. It also includes 59% of the genes from the edge/apothecia comparison. It also includes 12 genes unique to this set
venn_a2<-list(compared_to_center = ca_sig$target_id[ca_sig$change=="apothecium"],
               compared_to_edge = ea_sig$target_id[ea_sig$change=="apothecium"],
              compared_to_center_edge_pooled=a_sig$target_id[a_sig$change=="apothecium"])

a2<-ggVennDiagram(venn_a2,label_size = 5,set_size=5)+labs(title = "Upregulated in apothecia")+theme(title=element_text(size=12))+scale_x_continuous(expand = expansion(mult = .4))
a2

7. Visualize MAT expression

library(ComplexHeatmap)
library(viridis)
#make a matrix
tabd_df_a <- a_so$obs_norm[a_so$obs_norm$target_id %in% target_id,]
tabd_df_a <- dplyr::select(tabd_df_a, target_id, sample, 
            tpm)
tabd_df_a <- reshape2::dcast(tabd_df_a, target_id ~ sample, 
            value.var = "tpm") 
rownames(tabd_df_a) <- tabd_df_a$target_id
tabd_df_a$target_id <- NULL
trans_mat_a <- as.matrix(log(tabd_df_a + 1))

#make a top annotation
#define column annotations
s2c_a <- a_so$sample_to_covariates
s2c_a<-data.frame("sample"= colnames(tabd_df_a)) %>% left_join(s2c_a)
rownames(s2c_a)<-s2c_a$sample
s2c_a<-s2c_a %>% select(part)
ta_colors_a = c("apothecia" = "#619CFF", "thallus_edge" = "#F8766D","thallus_centre"="green")
ta_a = HeatmapAnnotation(df=s2c_a,col = list(condition = ta_colors_a))

#filter to include only MAT locus
filt_mat_MAT<-subset(trans_mat_a, rownames(trans_mat_a) %in% c("XANPAGTX0501_002103-T1","XANPAGTX0501_002104-T1"))
HM_mat = Heatmap(filt_mat_MAT, show_row_names = T, show_column_names = T,cluster_rows = T, row_title_rot = 0, col=viridis(100), heatmap_legend_param = list(title = "Expression: log(TPM)"), top_annotation = ta_a)

pdf(file="../results/MAT_heatmap.pdf",width=10,height=2)
draw(HM_mat)
dev.off()
## quartz_off_screen 
##                 2
HM_mat

* lolipop plot arranged by specimen

df<-data.frame(filt_mat_MAT) %>% mutate(target_id=rownames(filt_mat_MAT)) %>%
  pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
write.table(df, file="../analysis_and_temp_files/09_dge_architecture/mat_expression.txt", quote=F, sep='\t', row.names=F)

#only include thalli that a. have apothecia sample and b. have at least two samples
incl<-a_so$sample_to_covariates %>% mutate(if_apothecia=ifelse(part=="apothecia",T,F)) %>% 
  group_by(thallus) %>% summarize(n=n(),n_ap=sum(if_apothecia)) %>% filter(n>1,n_ap>0)
  
gg<-ggplot(df %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
  geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
  geom_point(stat = "identity",position=position_dodge(width = .5))+
  facet_grid(target_id~thallus)+
  xlab("")+ylab("Expression: log(TPM)")+
  theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45))+
  scale_color_manual( values = color_scheme)+
  theme(text=element_text(size=6),legend.position="bottom")

ggsave('../results/MAT_lopipop.pdf',gg, width = 4, height = 3)
gg

Investigate the most apothecia-upregulated proteins

  • XANPAGTX0501_001156-T3 is one variant of Sin3 transcriptional regulator
  • Only one is upregulated
filt_mat_sin3<-subset(trans_mat_a, rownames(trans_mat_a) %in% c("XANPAGTX0501_001156-T1","XANPAGTX0501_001156-T2","XANPAGTX0501_001156-T3"))
HM_sin3 = Heatmap(filt_mat_sin3, show_row_names = T, show_column_names = T,cluster_rows = T, row_title_rot = 0, col=viridis(100), heatmap_legend_param = list(title = "Expression: log(TPM)"), top_annotation = ta_a)
draw(HM_sin3)

df_sin3<-data.frame(filt_mat_sin3) %>% mutate(target_id=rownames(filt_mat_sin3)) %>%
  pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
## Joining with `by = join_by(sample)`
ggplot(df_sin3 %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
  geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
  geom_point(stat = "identity",position=position_dodge(width = .5))+
  facet_grid(target_id~thallus)+
  xlab("")+ylab("Expression: log(TPM)")+
  scale_color_manual( values = color_scheme)+
  theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45))

  • This is very interesting, but also inconsistent. Looked at the bam file but it didn’t clarify much

  • Visualize several key gene for the suppl. figure

    • XANPAGTX0501_004521-T1: Serine/threonine-protein kinase
    • XANPAGTX0501_001958-T1: Homeobox domain
    • XANPAGTX0501_003775-T1,XANPAGTX0501_004244-T1: argonaute
    • XANPAGTX0501_002123-T1: RNA-dependent RNA polymerase
    • XANPAGTX0501_004580-T1: Nuclear fusion protein Kar5
    • XANPAGTX0501_005735-T1: Conidiation-specific protein 6
    • XANPAGTX0501_004217-T1, XANPAGTX0501_002123-T1, XANPAGTX0501_002098-T1: RNA-binding domain
    • XANPAGTX0501_003213-T1, XANPAGTX0501_008856-T1, XANPAGTX0501_009316-T1, XANPAGTX0501_009942-T1, XANPAGTX0501_003212-T1, XANPAGTX0501_001643-T1: F-box
    • XANPAGTX0501_005815-T1,XANPAGTX0501_007869-T1,XANPAGTX0501_010380-T1: POZ
library(patchwork)
ap_genes<-c("XANPAGTX0501_004521-T1","XANPAGTX0501_001958-T1","XANPAGTX0501_004580-T1","XANPAGTX0501_005735-T1","XANPAGTX0501_002123-T1","XANPAGTX0501_003775-T1","XANPAGTX0501_004244-T1","XANPAGTX0501_004217-T1", "XANPAGTX0501_002098-T1")

filt_mat_ap<-subset(trans_mat_a, rownames(trans_mat_a) %in% ap_genes)
df_ap<-data.frame(filt_mat_ap) %>% mutate(target_id=rownames(filt_mat_ap)) %>%
  pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
df_ap$target_id<-factor(df_ap$target_id,levels=c("XANPAGTX0501_004521-T1","XANPAGTX0501_001958-T1","XANPAGTX0501_004580-T1","XANPAGTX0501_005735-T1","XANPAGTX0501_002123-T1","XANPAGTX0501_003775-T1","XANPAGTX0501_004244-T1",
    "XANPAGTX0501_004217-T1", "XANPAGTX0501_002098-T1") )

gg_ap<-ggplot(df_ap %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
  geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
  geom_point(stat = "identity",position=position_dodge(width = .5))+
  facet_grid(target_id~thallus)+
  xlab("")+ylab("Expression: log(TPM)")+
  theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45))+
  scale_color_manual( values = color_scheme)+
  theme(text=element_text(size=6))

ap_genes2<-c("XANPAGTX0501_003213-T1", "XANPAGTX0501_008856-T1", "XANPAGTX0501_009316-T1","XANPAGTX0501_009942-T1", "XANPAGTX0501_003212-T1", "XANPAGTX0501_001643-T1","XANPAGTX0501_005815-T1","XANPAGTX0501_007869-T1",
                    "XANPAGTX0501_010380-T1")

filt_mat_ap2<-subset(trans_mat_a, rownames(trans_mat_a) %in% ap_genes2)
df_ap2<-data.frame(filt_mat_ap2) %>% mutate(target_id=rownames(filt_mat_ap2)) %>%
  pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
df_ap2$target_id<-factor(df_ap2$target_id,levels=c("XANPAGTX0501_003213-T1", "XANPAGTX0501_008856-T1", "XANPAGTX0501_009316-T1","XANPAGTX0501_009942-T1", "XANPAGTX0501_003212-T1", "XANPAGTX0501_001643-T1","XANPAGTX0501_005815-T1","XANPAGTX0501_007869-T1",
                    "XANPAGTX0501_010380-T1") )

gg_ap2<-ggplot(df_ap2 %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
  geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
  geom_point(stat = "identity",position=position_dodge(width = .5))+
  facet_grid(target_id~thallus)+
  xlab("")+ylab("")+
  theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) +
  scale_color_manual( values = color_scheme)+
  theme(text=element_text(size=6))

gg_ap_all<-gg_ap+gg_ap2+ plot_layout(axis_titles = "collect",guides = 'collect')
ggsave('../results/apothecia_dge_lopipop.pdf',gg_ap_all, width = 8, height = 10)
  • Visualize a couple most interesting for the main figure on apothecia
#get the matrix for all samples, including culture
tabd_df<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/norm_counts_sleuth.txt")
rownames(tabd_df) <- tabd_df$target_id
tabd_df$target_id <- NULL
tabd_df <- mutate_all(tabd_df, function(x) as.numeric(as.character(x)))
trans_mat_08 <- as.matrix(log(tabd_df + 1))


selected_genes<-c("XANPAGTX0501_008856-T1","XANPAGTX0501_002123-T1")
#graph for the lichen samples
filt_mat_selected_thalli<-subset(trans_mat_a, rownames(trans_mat_a) %in% selected_genes)

df_thalli<-data.frame(filt_mat_selected_thalli) %>% mutate(target_id=rownames(filt_mat_selected_thalli)) %>%
  pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
## Joining with `by = join_by(sample)`
df_thalli$target_id<-factor(df_thalli$target_id,levels=c("XANPAGTX0501_008856-T1","XANPAGTX0501_002123-T1"))

gg_selected_thalli<-ggplot(df_thalli %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
  geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
  geom_point(stat = "identity",position=position_dodge(width = .5))+
  facet_grid(target_id~thallus)+
  xlab("")+ylab("Expression: log(TPM)")+
  theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) +
  scale_color_manual( values = color_scheme)+
  theme(text=element_text(size=6),legend.position = "bottom",
          axis.text.x = element_blank(),axis.ticks.x = element_blank())

#graph for the culture
filt_mat_selected_culture<-subset(trans_mat_08, rownames(trans_mat_08) %in% selected_genes)
df_culture<-data.frame(filt_mat_selected_culture) %>% mutate(target_id=rownames(filt_mat_selected_culture)) %>%
  pivot_longer(-target_id,names_to="sample",values_to="expression") %>%
  filter(!(sample %in% colnames(filt_mat_selected_thalli)))
df_culture$target_id<-factor(df_culture$target_id,levels=c("XANPAGTX0501_008856-T1","XANPAGTX0501_002123-T1"))

gg_selected_culture<-ggplot(df_culture, aes(y=expression,x=sample))+
  geom_segment( aes(x=sample, xend=sample, y=0, yend=expression))+
  geom_point(stat = "identity",position=position_dodge(width = .5))+
  facet_grid(target_id~.)+
  xlab("")+ylab("")+
  theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) + theme(text=element_text(size=6),axis.text = element_blank(),
                              axis.ticks = element_blank(),
                              axis.title.y = element_blank() )

ggsel<-gg_selected_thalli + gg_selected_culture + plot_layout(widths = c(0.6,0.4),nrow = 1) & scale_y_continuous(limits = c(0, 2.5))

#had to make one of them separately baceaus of the axes issue
selected_genes<-c("XANPAGTX0501_003775-T1")

#graph for the lichen samples
filt_mat_selected_thalli<-subset(trans_mat_a, rownames(trans_mat_a) %in% selected_genes)

df_thalli<-data.frame(filt_mat_selected_thalli) %>% mutate(target_id=rownames(filt_mat_selected_thalli)) %>%
  pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
## Joining with `by = join_by(sample)`
#df_thalli$target_id<-factor(df_selected$target_id,levels=c())

gg_selected_thalli<-ggplot(df_thalli %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
  geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
  geom_point(stat = "identity",position=position_dodge(width = .5))+
  facet_grid(target_id~thallus)+
  xlab("")+ylab("Expression: log(TPM)")+
  theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) +
  scale_color_manual( values = color_scheme)+
  theme(text=element_text(size=6),legend.position = "bottom",
      strip.background.x = element_blank(),strip.text.x = element_blank())

#graph for the culture
filt_mat_selected_culture<-subset(trans_mat_08, rownames(trans_mat_08) %in% selected_genes)
df_culture<-data.frame(filt_mat_selected_culture) %>% mutate(target_id=rownames(filt_mat_selected_culture)) %>%
  pivot_longer(-target_id,names_to="sample",values_to="expression") %>%
  filter(!(sample %in% colnames(filt_mat_selected_thalli)))
#df_thalli$target_id<-factor(df_selected$target_id,levels=c())

gg_selected_culture<-ggplot(df_culture, aes(y=expression,x=sample))+
  geom_segment( aes(x=sample, xend=sample, y=0, yend=expression))+
  geom_point(stat = "identity",position=position_dodge(width = .5))+
  facet_grid(target_id~.)+
  xlab("")+ylab("")+
  theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) + theme(text=element_text(size=6),axis.text.y = element_blank(),
                              axis.ticks.y = element_blank(),
                              axis.title.y = element_blank() )

ggsel2<-gg_selected_thalli + gg_selected_culture + plot_layout(widths = c(0.6,0.4),nrow = 1) & scale_y_continuous(limits = c(0, 5))

sel_final<-ggsel/plot_spacer()/ggsel2+ plot_layout(axis_titles = "collect",guides = "collect",heights = c(0.66,-0.155,0.34)) &theme(legend.position = "bottom")
ggsave('../results/selected_apothecia_dge_lopipop.pdf',sel_final, width = 7, height = 4)

sel_final

VIsualize interesting edge-upregulated genes

#get the matrix for all samples, including culture

selected_genes<-c("XANPAGTX0501_009376-T1","XANPAGTX0501_008852-T1")

#graph for the lichen samples
filt_mat_selected_thalli<-subset(trans_mat_a, rownames(trans_mat_a) %in% selected_genes)

df_thalli<-data.frame(filt_mat_selected_thalli) %>% mutate(target_id=rownames(filt_mat_selected_thalli)) %>%
  pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
## Joining with `by = join_by(sample)`
gg_selected_thalli<-ggplot(df_thalli %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
  geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
  geom_point(stat = "identity",position=position_dodge(width = .5))+
  facet_grid(target_id~thallus)+
  xlab("")+ylab("Expression: log(TPM)")+
  theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) +
  scale_color_manual( values = color_scheme)+
  theme(text=element_text(size=6),legend.position = "bottom",
              strip.background.x = element_blank(),strip.text.x = element_blank())

#graph for the culture
filt_mat_selected_culture<-subset(trans_mat_08, rownames(trans_mat_08) %in% selected_genes)
df_culture<-data.frame(filt_mat_selected_culture) %>% mutate(target_id=rownames(filt_mat_selected_culture)) %>%
  pivot_longer(-target_id,names_to="sample",values_to="expression") %>%
  filter(!(sample %in% colnames(filt_mat_selected_thalli)))


gg_selected_culture<-ggplot(df_culture, aes(y=expression,x=sample))+
  geom_segment( aes(x=sample, xend=sample, y=0, yend=expression))+
  geom_point(stat = "identity",position=position_dodge(width = .5))+
  facet_grid(target_id~.)+
  xlab("")+ylab("")+
  theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) + theme(text=element_text(size=6),axis.text.y = element_blank(),
                              axis.ticks.y = element_blank(),
                              axis.title.y = element_blank() )

ggsel<-gg_selected_thalli + gg_selected_culture + plot_layout(widths = c(0.6,0.4),nrow = 1) & scale_y_continuous(limits = c(0, 5))

#had to make one of them separately baceaus of the axes issue
selected_genes<-c("XANPAGTX0501_001015-T1")
selected_genes<-c("XANPAGTX0501_001643-T1")


#graph for the lichen samples
filt_mat_selected_thalli<-subset(trans_mat_a, rownames(trans_mat_a) %in% selected_genes)

df_thalli<-data.frame(filt_mat_selected_thalli) %>% mutate(target_id=rownames(filt_mat_selected_thalli)) %>%
  pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
## Joining with `by = join_by(sample)`
gg_selected_thalli<-ggplot(df_thalli %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
  geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
  geom_point(stat = "identity",position=position_dodge(width = .5))+
  facet_grid(target_id~thallus)+
  xlab("")+ylab("Expression: log(TPM)")+
  theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) +
  scale_color_manual( values = color_scheme)+
  theme(text=element_text(size=6),legend.position = "bottom",
        axis.text.x = element_blank(),
                              axis.ticks.x = element_blank(),
                              axis.title.x = element_blank() )

#graph for the culture
filt_mat_selected_culture<-subset(trans_mat_08, rownames(trans_mat_08) %in% selected_genes)
df_culture<-data.frame(filt_mat_selected_culture) %>% mutate(target_id=rownames(filt_mat_selected_culture)) %>%
  pivot_longer(-target_id,names_to="sample",values_to="expression") %>%
  filter(!(sample %in% colnames(filt_mat_selected_thalli)))
#df_thalli$target_id<-factor(df_selected$target_id,levels=c())

gg_selected_culture<-ggplot(df_culture, aes(y=expression,x=sample))+
  geom_segment( aes(x=sample, xend=sample, y=0, yend=expression))+
  geom_point(stat = "identity",position=position_dodge(width = .5))+
  facet_grid(target_id~.)+
  xlab("")+ylab("")+
  theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) + theme(text=element_text(size=6),axis.text = element_blank(),
                              axis.ticks = element_blank(),
                              axis.title = element_blank() )

ggsel2<-gg_selected_thalli + gg_selected_culture + plot_layout(widths = c(0.6,0.4),nrow = 1) & scale_y_continuous(limits = c(0, 7))

sel_final<-ggsel2/plot_spacer()/ggsel+ plot_layout(axis_titles = "collect",guides = "collect",heights = c(0.34,-0.105,0.66)) &theme(legend.position = "bottom")
ggsave('../results/selected_edge_dge_lopipop.pdf',sel_final, width = 7, height = 4)

sel_final

7. Compiling DGE table

ec_sig$Comparison<-"Edge / Center"
ea_sig$Comparison<-"Edge / Apothecia"
ca_sig$Comparison<-"Center / Apothecia"
a_sig$Comparison<-"Apothecia / Vegetative (edge + center)"

compiled<-rbind(ec_sig,ea_sig,ca_sig,a_sig) %>% filter(change!="low_logFC") %>%
  left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
  select(Comparison,change,target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho) %>% arrange(change) %>% arrange(Comparison)
write.table(compiled, file="../results/tissue_dge.txt", quote=F, sep='\t', row.names=F)

The gene that are upregulated in the center compared to the edge, are they also apothecia-upregulated?

  • All of them are at least in one apothecia-upregulated list
apothecia_up<-compiled$target_id[compiled$change=="apothecium"]
center_up<-ec_sig$target_id[ec_sig$change=="centre"]

ec_sig %>% filter(change=="centre") %>% 
  mutate(apothecia_upregulated = ifelse(target_id %in%apothecia_up,T,F)) %>%
  select(target_id,apothecia_upregulated,b)
## # A tibble: 9 × 3
##   target_id              apothecia_upregulated     b
##   <chr>                  <lgl>                 <dbl>
## 1 XANPAGTX0501_005615-T1 TRUE                  -1.01
## 2 XANPAGTX0501_005614-T1 TRUE                  -1.08
## 3 XANPAGTX0501_008007-T1 TRUE                  -1.16
## 4 XANPAGTX0501_002184-T1 TRUE                  -1.17
## 5 XANPAGTX0501_001949-T1 TRUE                  -1.19
## 6 XANPAGTX0501_002506-T1 TRUE                  -1.19
## 7 XANPAGTX0501_008856-T1 TRUE                  -1.28
## 8 XANPAGTX0501_009886-T1 TRUE                  -1.29
## 9 XANPAGTX0501_009927-T1 TRUE                  -1.62
  • All of them were in the apothecia/edge list
compiled %>% filter(change=="apothecium", target_id %in% center_up) %>%
   select(target_id,Comparison) %>% mutate(presence=1) %>%
  pivot_wider(names_from = Comparison,values_from = presence, values_fill=0)
## # A tibble: 9 × 4
##   target_id       Apothecia / Vegetati…¹ `Center / Apothecia` `Edge / Apothecia`
##   <chr>                            <dbl>                <dbl>              <dbl>
## 1 XANPAGTX0501_0…                      1                    0                  1
## 2 XANPAGTX0501_0…                      1                    1                  1
## 3 XANPAGTX0501_0…                      1                    0                  1
## 4 XANPAGTX0501_0…                      1                    1                  1
## 5 XANPAGTX0501_0…                      1                    1                  1
## 6 XANPAGTX0501_0…                      1                    1                  1
## 7 XANPAGTX0501_0…                      0                    0                  1
## 8 XANPAGTX0501_0…                      0                    0                  1
## 9 XANPAGTX0501_0…                      0                    0                  1
## # ℹ abbreviated name: ¹​`Apothecia / Vegetative (edge + center)`
  • per functional group, how many of the lichen-upregulated genes are also apothecia-upregulated
lichen_upr<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/upreg_in_lichen_sleuth.txt")
count_function<-ips_selected %>% filter(TranscriptID %in%lichen_upr$target_id) %>% group_by(Function) %>% summarize(total=n())
ips_selected %>% filter(TranscriptID %in% lichen_upr$target_id) %>%
  mutate(is_ap = ifelse(TranscriptID %in% apothecia_up,T,F)) %>%
  group_by(Function) %>% summarize(in_apothecia_up=sum(is_ap)) %>% left_join(count_function)
## Joining with `by = join_by(Function)`
## # A tibble: 19 × 3
##    Function                                  in_apothecia_up total
##    <chr>                                               <int> <int>
##  1 "Acetyl-CoA production and metabolism"                  1     4
##  2 "Carbohydrate storage"                                  1     1
##  3 "Cell division, proliferation and growth"               6    12
##  4 "Cell surface and cell wall proteins"                   2     9
##  5 "Cell wall biosynthesis "                               1     1
##  6 "Cell wall misc"                                        0     2
##  7 "Cell wall remodeling"                                  1     3
##  8 "Defense"                                               1     3
##  9 "G-proteins and GPCR"                                   0     1
## 10 "Lipid metabolism"                                      0     3
## 11 "Oxylipins"                                             0     2
## 12 "Protein ubiquitination"                                8    14
## 13 "RNA binding proteins"                                  4     5
## 14 "RNA interference"                                      3     3
## 15 "Ribosomal genes"                                       0     1
## 16 "Stress response genes"                                 0     1
## 17 "Transcription factors"                                 5    23
## 18 "Transporters"                                          0    27
## 19 "Velvet"                                                0     2
  • None of lichen-upregulated transporters are apothecia-upregulated!
  • Well, there is one protein we can id as a transporter that is upregulated in both, but in addition to that apothecia have 4 more that are not lichen upregulated!
compiled %>% filter(change=="apothecium", grepl("transporter",InterPro_new)) %>%
  filter(InterPro_new!="IPR004853 Sugar phosphate transporter domain",
         !grepl("ABC transporter-like",InterPro_new)) %>%
  select(target_id,InterPro_new,b,Comparison)  %>% 
  mutate(lichen_upregulated = ifelse(target_id %in%lichen_upr$target_id,T,F))
## # A tibble: 7 × 5
##   target_id              InterPro_new            b Comparison lichen_upregulated
##   <chr>                  <chr>               <dbl> <chr>      <lgl>             
## 1 XANPAGTX0501_001825-T1 IPR003663 Sugar/in… -1.06 Apothecia… FALSE             
## 2 XANPAGTX0501_010381-T1 IPR002293 Amino ac… -1.16 Apothecia… TRUE              
## 3 XANPAGTX0501_008594-T1 IPR036259 MFS tran… -1.04 Edge / Ap… FALSE             
## 4 XANPAGTX0501_000281-T1 IPR011701 Major fa… -1.28 Edge / Ap… FALSE             
## 5 XANPAGTX0501_001825-T1 IPR003663 Sugar/in… -1.40 Edge / Ap… FALSE             
## 6 XANPAGTX0501_009737-T1 IPR005829 Sugar tr… -1.54 Edge / Ap… FALSE             
## 7 XANPAGTX0501_010381-T1 IPR002293 Amino ac… -1.59 Edge / Ap… TRUE

Of the tisuue-DGE genes, what portion was lichen/culture DGE?

culture_upr<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/upreg_in_culture_sleuth.txt")
compiled %>% mutate(lichen_cult = case_when(
  target_id %in% lichen_upr$target_id ~ "upreg_lichen" ,
  target_id %in% culture_upr$target_id ~ "upreg_culture",
  T ~ "non_dge"
)) %>% group_by(Comparison,change,lichen_cult) %>%
  summarize(n=n()) %>%
  pivot_wider(names_from=lichen_cult,values_from = n,values_fill = 0) %>%
  mutate(total= upreg_lichen+upreg_culture+non_dge)
## `summarise()` has grouped output by 'Comparison', 'change'. You can override
## using the `.groups` argument.
## # A tibble: 7 × 6
## # Groups:   Comparison, change [7]
##   Comparison                     change non_dge upreg_culture upreg_lichen total
##   <chr>                          <chr>    <int>         <int>        <int> <int>
## 1 Apothecia / Vegetative (edge … apoth…      56            17          177   250
## 2 Apothecia / Vegetative (edge … thall…       0             1            1     2
## 3 Center / Apothecia             apoth…      21             7           90   118
## 4 Center / Apothecia             centre       0             0            1     1
## 5 Edge / Apothecia               apoth…     121            25          225   371
## 6 Edge / Apothecia               edge         3             1            9    13
## 7 Edge / Center                  centre       1             1            7     9
  • look at the culture-upregulated genes
compiled2 <- compiled %>% mutate(lichen_cult = case_when(
  target_id %in% lichen_upr$target_id ~ "upreg_lichen" ,
  target_id %in% culture_upr$target_id ~ "upreg_culture",
  T ~ "non_dge")) %>% 
  filter(lichen_cult=="upreg_culture")
compiled2 %>%  kable(format = "html", col.names = colnames(compiled2)) %>%
  kable_styling() %>%
  kableExtra::scroll_box(width = "100%", height = "400px")
Comparison change target_id b InterPro_new CAZyme_new Protease_new KO secreted_consensus lichen_ortho lichen_cult
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_007473-T1 -1.021407 NA NA NA FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_001223-T1 -1.064214 NA NA NA FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_009599-T1 -1.070929 NA NA NA FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_001948-T1 -1.099351 NA NA NA FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_006310-T1 -1.105045 IPR022137 Zinc finger protein, DUF3669 domain NA NA FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_001643-T1 -1.215746 IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily NA NA FALSE TRUE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_001952-T1 -1.257146 NA NA NA FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_001950-T1 -1.259001 NA NA NA FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_001951-T1 -1.262779 NA NA NA FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_001947-T1 -1.303157 NA NA NA FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_002165-T1 -1.325802 NA NA NA FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_002163-T1 -1.392989 NA NA NA FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_002164-T1 -1.582652 NA NA NA FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_009619-T1 -1.640066 NA NA NA FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_003209-T1 -1.709229 NA NA NA FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_009602-T1 -1.777131 NA NA NA FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) apothecium XANPAGTX0501_008109-T1 -2.159140 IPR004143 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain NA NA K03800 FALSE FALSE upreg_culture
Apothecia / Vegetative (edge + center) thallus XANPAGTX0501_009376-T1 2.496154 IPR043141 Ribosomal protein L10-like domain superfamily NA NA K02864 FALSE FALSE upreg_culture
Center / Apothecia apothecium XANPAGTX0501_002163-T1 -1.035184 NA NA NA FALSE FALSE upreg_culture
Center / Apothecia apothecium XANPAGTX0501_001947-T1 -1.046488 NA NA NA FALSE FALSE upreg_culture
Center / Apothecia apothecium XANPAGTX0501_001951-T1 -1.118810 NA NA NA FALSE FALSE upreg_culture
Center / Apothecia apothecium XANPAGTX0501_003209-T1 -1.170208 NA NA NA FALSE FALSE upreg_culture
Center / Apothecia apothecium XANPAGTX0501_009602-T1 -1.212068 NA NA NA FALSE FALSE upreg_culture
Center / Apothecia apothecium XANPAGTX0501_009619-T1 -1.314627 NA NA NA FALSE FALSE upreg_culture
Center / Apothecia apothecium XANPAGTX0501_008109-T1 -2.657633 IPR004143 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain NA NA K03800 FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_005583-T1 -1.079779 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_000885-T1 -1.108859 IPR036305 RGS domain superfamily NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_010011-T1 -1.134493 IPR036013 Band 7/SPFH domain superfamily NA NA K07192 FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_009812-T1 -1.143459 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_009785-T1 -1.191020 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_009599-T1 -1.242828 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_003864-T1 -1.363940 IPR009075 Acyl-CoA dehydrogenase/oxidase C-terminal, IPR009100 Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily, IPR013786 Acyl-CoA dehydrogenase/oxidase, N-terminal, IPR036250 Acyl-CoA dehydrogenase-like, C-terminal, IPR037069 Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_007473-T1 -1.375934 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_007936-T1 -1.379176 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_005640-T1 -1.380432 IPR013087 Zinc finger C2H2-type NA NA FALSE TRUE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_009761-T1 -1.387848 IPR001283 Cysteine-rich secretory protein-related, IPR014044 CAP domain, IPR018244 Allergen V5/Tpx-1-related, conserved site, IPR034120 None, IPR035940 CAP superfamily NA NA K20412 TRUE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_001951-T1 -1.498238 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_009737-T1 -1.540774 IPR005829 Sugar transporter, conserved site, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_001948-T1 -1.662753 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_001950-T1 -1.678963 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_001949-T1 -1.732732 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_001947-T1 -1.767840 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_002163-T1 -1.904022 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_001643-T1 -1.910689 IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily NA NA FALSE TRUE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_002165-T1 -1.959472 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_001952-T1 -2.002699 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_009619-T1 -2.203533 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_003209-T1 -2.437600 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_009602-T1 -2.500879 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia apothecium XANPAGTX0501_002164-T1 -2.527734 NA NA NA FALSE FALSE upreg_culture
Edge / Apothecia edge XANPAGTX0501_006869-T1 1.099929 IPR008979 Galactose-binding-like domain superfamily, IPR017853 Glycoside hydrolase superfamily, IPR024655 Asl1-like, glycosyl hydrolase catalytic domain GH128 NA TRUE FALSE upreg_culture
Edge / Center centre XANPAGTX0501_001949-T1 -1.187615 NA NA NA FALSE FALSE upreg_culture